Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006746.1 Kokia drynarioides strain JFW-HI SEQ_121344, 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: 29848
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Warning! 141 characters in sequence are not A, C, G, or T
Found at i:3173 original size:13 final size:13
Alignment explanation
Indices: 3155--3179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3145 AATATATTTA
3155 TTAATTAAAAATT
1 TTAATTAAAAATT
3168 TTAATTAAAAAT
1 TTAATTAAAAAT
3180 AAAAAATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATTAAAAATT
Found at i:4796 original size:80 final size:81
Alignment explanation
Indices: 4647--4802 Score: 287
Period size: 81 Copynumber: 1.9 Consensus size: 81
4637 AAAGTTGGTA
* *
4647 GTTATTTTTTTAATAATATACTTTTTAAAATTTGAATTGTGTTTCTTTTTTTCAAAATGCAATGT
1 GTTATTTTTTTAATAATATACTTTTTAAAAATTGAATTGTGTTTCTTTTTTTCAAAATACAATGT
4712 ACCTTATTATTACACT
66 ACCTTATTATTACACT
4728 GTTATTTTTTTAATAATATACTTTTTAAAAATTGAATTGTGTTTC-TTTTTTCAAAATACAATGT
1 GTTATTTTTTTAATAATATACTTTTTAAAAATTGAATTGTGTTTCTTTTTTTCAAAATACAATGT
4792 ACCTTATTATT
66 ACCTTATTATT
4803 CACCAAAAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 29 0.40
81 44 0.60
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (81 bp):
GTTATTTTTTTAATAATATACTTTTTAAAAATTGAATTGTGTTTCTTTTTTTCAAAATACAATGT
ACCTTATTATTACACT
Found at i:5092 original size:7 final size:7
Alignment explanation
Indices: 5072--5104 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5062 TCCATCAATC
5072 TTAAAAT
1 TTAAAAT
5079 CTTAAAAT
1 -TTAAAAT
5087 TTAAAAT
1 TTAAAAT
5094 TTAAAAT
1 TTAAAAT
5101 TTAA
1 TTAA
5105 TTTCAGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:13556 original size:18 final size:18
Alignment explanation
Indices: 13533--13569 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13523 CTAAATCTTT
13533 ATTTTAATATTAGTATAC
1 ATTTTAATATTAGTATAC
* *
13551 ATTTTAATTTTATTATAC
1 ATTTTAATATTAGTATAC
13569 A
1 A
13570 CATTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTAATATTAGTATAC
Found at i:17635 original size:7 final size:7
Alignment explanation
Indices: 17625--17649 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17615 CTCTAAACCT
17625 TAAATTC
1 TAAATTC
17632 TAAATTC
1 TAAATTC
17639 TAAATTC
1 TAAATTC
17646 TAAA
1 TAAA
17650 CCAGAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATTC
Found at i:23451 original size:89 final size:89
Alignment explanation
Indices: 23297--23475 Score: 331
Period size: 89 Copynumber: 2.0 Consensus size: 89
23287 CCCCCCCAGT
* * *
23297 CGAGAGGAAGATTATAAAATGGCTTGCCTCAAAACAATCTATAGTTAGCTTGAACAAGTGGTAGT
1 CGAGAGGAAGATTATAAAATGGCTTGCCCCAAAACAATCTATAGTTAACTTGAACAAGTGATAGT
23362 TATCATAAGAGAAACAGAGAGTGG
66 TATCATAAGAGAAACAGAGAGTGG
23386 CGAGAGGAAGATTATAAAATGGCTTGCCCCAAAACAATCTATAGTTAACTTGAACAAGTGATAGT
1 CGAGAGGAAGATTATAAAATGGCTTGCCCCAAAACAATCTATAGTTAACTTGAACAAGTGATAGT
23451 TATCATAAGAGAAACAGAGAGTGG
66 TATCATAAGAGAAACAGAGAGTGG
23475 C
1 C
23476 TCAGAATATT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (89 bp):
CGAGAGGAAGATTATAAAATGGCTTGCCCCAAAACAATCTATAGTTAACTTGAACAAGTGATAGT
TATCATAAGAGAAACAGAGAGTGG
Found at i:25942 original size:14 final size:14
Alignment explanation
Indices: 25923--25957 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
25913 CTTCTTTTCT
25923 TTCTTCCAATAATA
1 TTCTTCCAATAATA
25937 TTCTTCCAATAATA
1 TTCTTCCAATAATA
25951 TTCTTCC
1 TTCTTCC
25958 CTCACAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.46
Consensus pattern (14 bp):
TTCTTCCAATAATA
Found at i:27481 original size:96 final size:96
Alignment explanation
Indices: 27307--27488 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 96
27297 AAGAATGTTT
* ** *
27307 GATTATCTCGATTTGAGGAAAGGTTGCACATAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACATAGTAAATTAAGGCGCAAATTTTCAGAATCGAAGA
*
27372 TATGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAGGAAACATTGCCTCGATTAAGGGTATTC
* *
27403 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAATTAAGGCGCAAATTTTC-GAAACTCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACATAGTAAATTAAGGCGCAAATTTTCAG-AA-TCGAA
*
27467 -ATAA-GAGAATATTGCCTCGATT
64 GATAAGGA-AACATTGCCTCGATT
27489 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 3 0.04
96 67 0.89
97 5 0.07
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACATAGTAAATTAAGGCGCAAATTTTCAGAATCGAAGA
TAAGGAAACATTGCCTCGATTAAGGGTATTC
Found at i:27856 original size:58 final size:59
Alignment explanation
Indices: 27785--27899 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 59
27775 TTAGGGGTTA
* * *
27785 AAAATGGACTTTTTAGACATTCGGGGGTAAAAGGGTA-ATTTTGAGAGTTTCGAGGTCG
1 AAAATGGACTTTTTAGACATTCGAGGGAAAAAGGGTATATTTTGAAAGTTTCGAGGTCG
* * * *
27843 AAAATGGAGTTTTTGGAGATTCGAGGGAAAAAGGGTATTTTTTGAAAGTTTCGAGGT
1 AAAATGGACTTTTTAGACATTCGAGGGAAAAAGGGTATATTTTGAAAGTTTCGAGGT
27900 AAAAAATGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 32 0.65
59 17 0.35
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.32
Consensus pattern (59 bp):
AAAATGGACTTTTTAGACATTCGAGGGAAAAAGGGTATATTTTGAAAGTTTCGAGGTCG
Found at i:27865 original size:29 final size:28
Alignment explanation
Indices: 27823--28094 Score: 251
Period size: 29 Copynumber: 9.2 Consensus size: 28
27813 AAAAGGGTAA
* *
27823 TTTTGAGAGTTTCGAGGTCGAAAATGGAGT
1 TTTTG-GAGTTTCGAGGT-AAAAATGGAAT
* * * *
27853 TTTTGGAGATTCGAGGGAAAAAGGGTATT
1 TTTTGGAGTTTCGAGGTAAAAATGG-AAT
* * *
27882 TTTTGAAAGTTTCGAGGTAAAAAATGAAAA
1 TTTTG-GAGTTTCGAGGT-AAAAATGGAAT
*
27912 TTTTGGAGGTTCGAGGGTAAAAATGGAAT
1 TTTTGGAGTTTCGA-GGTAAAAATGGAAT
27941 TTTTGGGAGTTTCGAGGTAAAAATGGAAT
1 TTTT-GGAGTTTCGAGGTAAAAATGGAAT
27970 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTGG-AGTTTCGAGGT-AAAAATGGAAT
*
28000 TTTTGGAAG-TTAGAGGGTAAAAATGGAAT
1 TTTTGG-AGTTTCGA-GGTAAAAATGGAAT
*
28029 TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
1 TTTTGG-AGTTTCGAGGT-AAAAATGGAAT
* * * *
28059 TTTTAGAAGTTTAG-GGATAAAAATAGATT
1 TTTT-GGAGTTTCGAGG-TAAAAATGGAAT
28088 TTTTGGA
1 TTTTGGA
28095 TAGATTAGGG
Statistics
Matches: 205, Mismatches: 25, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
28 10 0.05
29 108 0.53
30 80 0.39
31 7 0.03
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTGGAGTTTCGAGGTAAAAATGGAAT
Found at i:27916 original size:59 final size:57
Alignment explanation
Indices: 27783--28035 Score: 240
Period size: 59 Copynumber: 4.3 Consensus size: 57
27773 AATTAGGGGT
* * * * * *
27783 TAAAAATGGACTTTTTAGACATTCGGGGGTAAAAGGGTAATTTTGAGAGTTTCGAGG
1 TAAAAATGGAATTTTTGGAGATTCGAGGGAAAAAGGGTATTTTTGAGAGTTTCGAGG
* * *
27840 TCGAAAATGGAGTTTTTGGAGATTCGAGGGAAAAAGGGTATTTTTTGAAAGTTTCGAGG
1 T-AAAAATGGAATTTTTGGAGATTCGAGGGAAAAAGGGTA-TTTTTGAGAGTTTCGAGG
* * * * * *
27899 TAAAAAATGAAAATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGAGG
1 T-AAAAATGGAATTTTTGGAGATTCGAGGG-AAAAAGGGTATTTTTGAGAGTTTCGAGG
* * * * *
27958 TAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTG-GAAG-TTAGAGGG
1 TAAAAATGGAATTTTTGG-AGATTCGAGG-GAAAAAGGGTATTTTTGAG-AGTTTCGA-GG
28017 TAAAAATGGAATTTTTGGA
1 TAAAAATGGAATTTTTGGA
28036 AGTTTCGGGG
Statistics
Matches: 166, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
57 1 0.01
58 53 0.32
59 104 0.63
60 8 0.05
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (57 bp):
TAAAAATGGAATTTTTGGAGATTCGAGGGAAAAAGGGTATTTTTGAGAGTTTCGAGG
Found at i:27936 original size:88 final size:87
Alignment explanation
Indices: 27821--28070 Score: 272
Period size: 88 Copynumber: 2.8 Consensus size: 87
27811 GTAAAAGGGT
* * * *
27821 AATTTTGAGAGTTTCGA-GGTCGAAAATGGAGTTTTTGGAGATTCGAGGGAAAAAGGGTATTTTT
1 AATTTTG-GAGGTTCGAGGGT-AAAAATGGAATTTTTGGAGATTCGAGGGAAAAAGGG-AATTTT
27885 TGAAAGTTTCGAGGTAAAAAATGAA
63 TGAAAGTTTCGAGGTAAAAAATGAA
* * *
27910 AATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGAGGTAAAAATGGAATTTTTG
1 AATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTT-GGAGATTCGAGGGAAAAAGGGAATTTTTG
* * *
27975 GAAGTTTCGAGGTCAAAAATGGA
65 AAAGTTTCGAGGTAAAAAATGAA
* * * * *
27998 ATTTTTGGAAGTTAGAGGGTAAAAATGGAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTT
1 AATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTTGG-AGATTCGAGGG--AAAAAGGGAATTTT
28062 T-AGAAGTTT
63 TGA-AAGTTT
28071 AGGGATAAAA
Statistics
Matches: 140, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
87 4 0.03
88 87 0.62
89 49 0.35
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (87 bp):
AATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTTGGAGATTCGAGGGAAAAAGGGAATTTTTGA
AAGTTTCGAGGTAAAAAATGAA
Found at i:28036 original size:59 final size:59
Alignment explanation
Indices: 27843--28094 Score: 273
Period size: 59 Copynumber: 4.3 Consensus size: 59
27833 TTCGAGGTCG
* * * * * * *
27843 AAAATGGAGTTTTTGG-AGATTCGAGG-GAAAAAGGGTATTTTTTGAAAGTTTCGAGGTAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGG-AATTTTTGGAAGTTTAGAGGT-A
* * * * *
27902 AAAATGAAAATTTTGG-AGGTTCGAGGGT-AAAAATGGAATTTTTGGGAGTTTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTTAGAGGTA
27960 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG-TTAGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAGA-GGTA
* *
28019 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTTTAG-GGATA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAGAGG-TA
* *
28078 AAAATAGATTTTTTGGA
1 AAAATGGAATTTTTGGA
28095 TAGATTAGGG
Statistics
Matches: 169, Mismatches: 17, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
58 24 0.14
59 132 0.78
60 13 0.08
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAGAGGTA
Done.