Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011891.1 Kokia drynarioides strain JFW-HI SEQ_126888, 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: 60279
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 125 characters in sequence are not A, C, G, or T
Found at i:3693 original size:12 final size:13
Alignment explanation
Indices: 3667--3699 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3657 GTAAAAAGGA
*
3667 GCAAAGAACATAG
1 GCAAAGAACAGAG
3680 GCAAA-AACAGAG
1 GCAAAGAACAGAG
3692 GCAAAGAA
1 GCAAAGAA
3700 ACAGGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.15, G:0.24, T:0.03
Consensus pattern (13 bp):
GCAAAGAACAGAG
Found at i:4026 original size:3 final size:3
Alignment explanation
Indices: 4020--4086 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
4010 ATCATTTATT
* * * *
4020 ATA ATAA ATA ACA TTA ATA ATA ATA ATA ATA ATA A-A TATA ACA TTA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
*
4066 ATA ATA TTA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
4087 AAAAAAGGGA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 3 0.06
3 43 0.86
4 4 0.08
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7742 original size:2 final size:2
Alignment explanation
Indices: 7735--7761 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7725 ACACTTAAAG
7735 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7762 TGGTAGTTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17529 original size:16 final size:17
Alignment explanation
Indices: 17505--17538 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17495 TTCTCAGAAA
17505 TAACCCTCTC-CATCCC
1 TAACCCTCTCACATCCC
*
17521 TAACTCTCTCACATCCC
1 TAACCCTCTCACATCCC
17538 T
1 T
17539 CTTTTCCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.21, C:0.50, G:0.00, T:0.29
Consensus pattern (17 bp):
TAACCCTCTCACATCCC
Found at i:29526 original size:25 final size:23
Alignment explanation
Indices: 29479--29525 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
29469 CTACAAAAAA
29479 AAAAAGGGTAAAAGGTTTTTTTT
1 AAAAAGGGTAAAAGGTTTTTTTT
*
29502 NAAAAAGGGTAAAAGATTTTTTTT
1 -AAAAAGGGTAAAAGGTTTTTTTT
29526 TTTTTTGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.38
Consensus pattern (23 bp):
AAAAAGGGTAAAAGGTTTTTTTT
Found at i:31730 original size:78 final size:78
Alignment explanation
Indices: 31601--31753 Score: 306
Period size: 78 Copynumber: 2.0 Consensus size: 78
31591 GCTAGACCAG
31601 ATATCATGCAGCTATGGGTTGGGTGCGTTTCTAAATTAACTTGGACACTATAAGTTTAGTACATG
1 ATATCATGCAGCTATGGGTTGGGTGCGTTTCTAAATTAACTTGGACACTATAAGTTTAGTACATG
31666 TTGAGTGAAGCAA
66 TTGAGTGAAGCAA
31679 ATATCATGCAGCTATGGGTTGGGTGCGTTTCTAAATTAACTTGGACACTATAAGTTTAGTACATG
1 ATATCATGCAGCTATGGGTTGGGTGCGTTTCTAAATTAACTTGGACACTATAAGTTTAGTACATG
31744 TTGAGTGAAG
66 TTGAGTGAAG
31754 GATTTAAAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (78 bp):
ATATCATGCAGCTATGGGTTGGGTGCGTTTCTAAATTAACTTGGACACTATAAGTTTAGTACATG
TTGAGTGAAGCAA
Found at i:35118 original size:19 final size:19
Alignment explanation
Indices: 35096--35139 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
35086 TTAAAAAGTA
*
35096 TTTAATATTACAATTTT-AT
1 TTTAATAATA-AATTTTAAT
35115 TTTAATAATAAATTTTAAT
1 TTTAATAATAAATTTTAAT
35134 TTTAAT
1 TTTAAT
35140 TTATAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATAATAAATTTTAAT
Found at i:43264 original size:29 final size:30
Alignment explanation
Indices: 43208--43273 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
43198 ATTTTCAAGG
* *
43208 AATTTGGGGATCAAAATTGAAATTTTTGGAA
1 AATTT-GGGATCAAAATCGAAACTTTTGGAA
*
43239 AATTTGGGATTAAAATCG-AACTTTTGGAA
1 AATTTGGGATCAAAATCGAAACTTTTGGAA
43268 AATTTG
1 AATTTG
43274 AGGTCGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 16 0.50
30 11 0.34
31 5 0.16
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
AATTTGGGATCAAAATCGAAACTTTTGGAA
Found at i:43292 original size:29 final size:29
Alignment explanation
Indices: 43260--43557 Score: 202
Period size: 30 Copynumber: 10.1 Consensus size: 29
43250 AAAATCGAAC
43260 TTTTGGAAAA-TTTGAGGTCGAAAATGTGA
1 TTTTGGAAAAGTTTGAGGTC-AAAATGTGA
* *
43289 TTTTTGG-AAA-TTTGAGG-GAAAATGGGA
1 -TTTTGGAAAAGTTTGAGGTCAAAATGTGA
*
43316 TTTT-GAAGAAGTTTGGGGTCAAAATGTGA
1 TTTTGGAA-AAGTTTGAGGTCAAAATGTGA
*
43345 TTTTGGAGAAGTTT-AGCAGTCAAAATGTGA
1 TTTTGGAAAAGTTTGAG--GTCAAAATGTGA
43375 TTTTGGAAAAGTTTTG-GGCTCAAAATGTGA
1 TTTTGGAAAAG-TTTGAGG-TCAAAATGTGA
* * *
43405 TTTT-GATAAAGTTTTAAGGTTAAAATATGA
1 TTTTGGA-AAAG-TTTGAGGTCAAAATGTGA
* * *
43435 TTTTAGAAAAGTTT-AGGGATTAAAATGTAA
1 TTTTGGAAAAGTTTGA-GG-TCAAAATGTGA
* *
43465 TTTTGGAAAATTTTTG-GGTTGAAAATGTGA
1 TTTTGGAAAA-GTTTGAGG-TCAAAATGTGA
* * * * *
43495 TTTTAGAAAATTTTAGGGGTTAAAATGTTA
1 TTTTGGAAAAGTTT-GAGGTCAAAATGTGA
* ** **
43525 TTTTAGAAACTTTTGAGGTCAAAACATGA
1 TTTTGGAAAAGTTTGAGGTCAAAATGTGA
43554 TTTT
1 TTTT
43558 TAGAAGTTTA
Statistics
Matches: 222, Mismatches: 27, Indels: 39
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.00
26 5 0.02
27 10 0.05
28 8 0.04
29 54 0.24
30 131 0.59
31 13 0.06
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
TTTTGGAAAAGTTTGAGGTCAAAATGTGA
Found at i:43317 original size:27 final size:29
Alignment explanation
Indices: 43229--43319 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
43219 CAAAATTGAA
** * *
43229 ATTTTTGGAAAATTTG-GGATTAAAATCGA
1 ATTTTTGGAAAATTTGAGG-CGAAAATGGG
* *
43258 ACTTTTGGAAAATTTGAGGTCGAAAATGTG
1 ATTTTTGGAAAATTTGAGG-CGAAAATGGG
43288 ATTTTTGG-AAATTTGAGG-GAAAATGGG
1 ATTTTTGGAAAATTTGAGGCGAAAATGGG
43315 ATTTT
1 ATTTT
43320 GAAGAAGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
27 13 0.25
29 25 0.48
30 14 0.27
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
ATTTTTGGAAAATTTGAGGCGAAAATGGG
Found at i:43450 original size:90 final size:90
Alignment explanation
Indices: 43336--43533 Score: 249
Period size: 90 Copynumber: 2.2 Consensus size: 90
43326 GTTTGGGGTC
* * *
43336 AAAATGTGATTTTGGAGAAGTTTAGCAG-TCAAAATGTGATTTTGGAAAAGTTTTGGGCTCAAAA
1 AAAATGTGATTTTAGAAAAGTTTAG-AGATCAAAATGTAATTTTGGAAAAGTTTTGGGCTCAAAA
43400 TGTGATTTT-GATAAAGTTTTA-AGGTT
65 TGTGATTTTAGA-AAA-TTTTAGAGGTT
* * * * * *
43426 AAAATATGATTTTAGAAAAGTTTAGGGATTAAAATGTAATTTTGGAAAATTTTTGGGTTGAAAAT
1 AAAATGTGATTTTAGAAAAGTTTAGAGATCAAAATGTAATTTTGGAAAAGTTTTGGGCTCAAAAT
*
43491 GTGATTTTAGAAAATTTTAGGGGTT
66 GTGATTTTAGAAAATTTTAGAGGTT
*
43516 AAAATGTTATTTTAGAAA
1 AAAATGTGATTTTAGAAA
43534 CTTTTGAGGT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
89 6 0.06
90 85 0.91
91 2 0.02
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (90 bp):
AAAATGTGATTTTAGAAAAGTTTAGAGATCAAAATGTAATTTTGGAAAAGTTTTGGGCTCAAAAT
GTGATTTTAGAAAATTTTAGAGGTT
Found at i:44479 original size:10 final size:10
Alignment explanation
Indices: 44461--44532 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
44451 AAACTTCTTT
44461 TTTATTATTA
1 TTTATTATTA
44471 TTTA--A-TA
1 TTTATTATTA
*
44478 TTAATTATTA
1 TTTATTATTA
*
44488 -TTATTAGGTA
1 TTTATTA-TTA
*
44498 TTTATTACTA
1 TTTATTATTA
44508 TATT-TTATTA
1 T-TTATTATTA
44518 TTTATTAATTA
1 TTTATT-ATTA
44529 TTTA
1 TTTA
44533 CTAAAACACT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 8 0.16
10 19 0.39
11 16 0.33
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTATTATTA
Found at i:55764 original size:79 final size:79
Alignment explanation
Indices: 55633--55793 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 79
55623 ACTGTAAAAC
*
55633 AGATATAAAGAATACTAAAACAAGTGATCTTGCGTTTTAAAAAAAGCAGAAATCTATAATAAGCA
1 AGATATAAAGAATACTAAAACAAGTGATCTTGCATTTTAAAAAAAGCAGAAATCTATAATAAGCA
55698 AAACATCATTGGTG
66 AAACATCATTGGTG
* *
55712 AGATATGAAGAATACTAAAACAAGTGATCTTGCATTTTACAAAAAGCAGAAATCTATAATAAGCA
1 AGATATAAAGAATACTAAAACAAGTGATCTTGCATTTTAAAAAAAGCAGAAATCTATAATAAGCA
55777 AAACATCATTGGTG
66 AAACATCATTGGTG
55791 AGA
1 AGA
55794 AGCTAACCTA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (79 bp):
AGATATAAAGAATACTAAAACAAGTGATCTTGCATTTTAAAAAAAGCAGAAATCTATAATAAGCA
AAACATCATTGGTG
Done.