Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013445.1 Kokia drynarioides strain JFW-HI SEQ_128471, 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: 74230
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3307 original size:20 final size:20
Alignment explanation
Indices: 3282--3330 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
3272 ATTAAGCTTA
3282 TTCAAAATATAGATTTATAT
1 TTCAAAATATAGATTTATAT
3302 TTCAAAATATAGATTTATAT
1 TTCAAAATATAGATTTATAT
3322 TTCAAAATA
1 TTCAAAATA
3331 AAATATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (20 bp):
TTCAAAATATAGATTTATAT
Found at i:4053 original size:28 final size:28
Alignment explanation
Indices: 3998--4064 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
3988 AATTTTAATG
*
3998 GTAAAATTGTATTTTTTTTTTAATAAAA
1 GTAAAATTGTATTTTTTTTCTAATAAAA
*
4026 GTAAAATTGTATTTTAATTTTCTAAAAAATA
1 GTAAAATTGTATTTT--TTTTCTAATAAA-A
*
4057 ATAAAATT
1 GTAAAATT
4065 TTAATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 15 0.45
30 10 0.30
31 8 0.24
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (28 bp):
GTAAAATTGTATTTTTTTTCTAATAAAA
Found at i:8894 original size:41 final size:41
Alignment explanation
Indices: 8834--8911 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
8824 AGAGCCAAGA
*
8834 AAAGGAAAAGAGAAGCAAGAAACTCACAAAGGGGACAGGAC
1 AAAGGAAAAGAGAACCAAGAAACTCACAAAGGGGACAGGAC
**
8875 AAAGGAAAAGAGAACCAAGAAACTCGTAAAGGGGACA
1 AAAGGAAAAGAGAACCAAGAAACTCACAAAGGGGACA
8912 AGACCATTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.54, C:0.14, G:0.28, T:0.04
Consensus pattern (41 bp):
AAAGGAAAAGAGAACCAAGAAACTCACAAAGGGGACAGGAC
Found at i:27465 original size:2 final size:2
Alignment explanation
Indices: 27458--27483 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27448 AATTTAAATA
27458 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
27484 TTACAAAGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28062 original size:23 final size:21
Alignment explanation
Indices: 28036--28087 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
28026 AGTTTAATTG
28036 AAAAAATATTAAAAAAAGTAAA
1 AAAAAATATTAAAAAAAG-AAA
* *
28058 TAAAAAAAATTAAAAATAGAAA
1 -AAAAAATATTAAAAAAAGAAA
28080 AAAAAATA
1 AAAAAATA
28088 GGTTGAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
22 3 0.12
23 16 0.62
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAAATATTAAAAAAAGAAA
Found at i:28072 original size:21 final size:19
Alignment explanation
Indices: 28048--28086 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
28038 AAAATATTAA
28048 AAAAAGTAAATAAAAAAAATT
1 AAAAA-TAAA-AAAAAAAATT
*
28069 AAAAATAGAAAAAAAAAT
1 AAAAATAAAAAAAAAAAT
28087 AGGTTGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAATAAAAAAAAAAATT
Found at i:32797 original size:19 final size:19
Alignment explanation
Indices: 32775--32816 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
32765 GATGGAAATA
32775 AATTAAATTCATTTT-TTTT
1 AATTAAATT-ATTTTCTTTT
*
32794 AATTGAATTATTTTCTTTT
1 AATTAAATTATTTTCTTTT
32813 AATT
1 AATT
32817 CATGACGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTAAATTATTTTCTTTT
Found at i:33352 original size:108 final size:106
Alignment explanation
Indices: 33240--33453 Score: 306
Period size: 108 Copynumber: 2.0 Consensus size: 106
33230 CAAATTTTTT
* ** *
33240 AAGAA-AAGCAATTAAACTCCTAT-TTTTTTTTTTTTTTTTTNGCACTCACTTGGATACTTGAAC
1 AAGAAGAAGCAATTAAAC-CCT-TCTTTTTTTTTTTTTTTTT-GCACTCAATTGGATAAATAAAC
*
33303 ATTCAAAATACATCAAAAAGACCCTCAAACTTTTTCAAAAAAAAG
63 ATTCAAAATACATC-AAAAGACCATCAAACTTTTTCAAAAAAAAG
*
33348 AAGAAGAAGCAATTAAACCCTTGCTTTTTTTTTTTTTTTTTGCACTCAATTGGATAAATAAACTT
1 AAGAAGAAGCAATTAAACCCTT-CTTTTTTTTTTTTTTTTTGCACTCAATTGGATAAATAAACAT
*
33413 TCAAAATGCATCAAAAGACCATCAAACTTTTTCAAAAAAAA
65 TCAAAATACATCAAAAGACCATCAAACTTTTTCAAAAAAAA
33454 AATTAAACCC
Statistics
Matches: 96, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
107 29 0.30
108 38 0.40
109 29 0.30
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (106 bp):
AAGAAGAAGCAATTAAACCCTTCTTTTTTTTTTTTTTTTTGCACTCAATTGGATAAATAAACATT
CAAAATACATCAAAAGACCATCAAACTTTTTCAAAAAAAAG
Found at i:33610 original size:9 final size:10
Alignment explanation
Indices: 33588--33621 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
33578 GACATGTGAC
*
33588 AAAAACTTAT
1 AAAAAATTAT
*
33598 AAAAAATTAA
1 AAAAAATTAT
33608 AAAAAATTAT
1 AAAAAATTAT
33618 AAAA
1 AAAA
33622 TGCATCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:38831 original size:37 final size:38
Alignment explanation
Indices: 38790--38861 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
38780 ATAATTTAAG
38790 CTTAAAAGAACTCA-TTAACTGTGTAATTTATACATAA
1 CTTAAAAGAACTCATTTAACTGTGTAATTTATACATAA
38827 CTTAAAAGAACTCATTTAACTGTGTAATTTATACA
1 CTTAAAAGAACTCATTTAACTGTGTAATTTATACA
38862 AAATTGTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 14 0.41
38 20 0.59
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (38 bp):
CTTAAAAGAACTCATTTAACTGTGTAATTTATACATAA
Found at i:40390 original size:3 final size:3
Alignment explanation
Indices: 40382--40456 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
40372 CTATTAATTC
40382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
40430 GAT GAT AAT GAT AAT GAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
40457 TATTATGGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43285 original size:75 final size:75
Alignment explanation
Indices: 43192--43342 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
43182 CAGCCTACCG
* *
43192 TTCACACCATTAGAGACTAATTTATCCCTTTACCGTGAAAATTTCATCAAAGTACCCTTCTTTCA
1 TTCACACAATTAGAGACTAATTTATCCCTTTACCATGAAAATTTCATCAAAGTACCCTTCTTTCA
*
43257 GTAAAATAAT
66 GTAAAAAAAT
* *
43267 TTCACACAATTAGTGACTAATTTATCCCTTTACCATGAAAATTTCATCAAAGTACCTTTCTTTCA
1 TTCACACAATTAGAGACTAATTTATCCCTTTACCATGAAAATTTCATCAAAGTACCCTTCTTTCA
43332 GTAAAAAAAT
66 GTAAAAAAAT
43342 T
1 T
43343 CCAACAAAGT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (75 bp):
TTCACACAATTAGAGACTAATTTATCCCTTTACCATGAAAATTTCATCAAAGTACCCTTCTTTCA
GTAAAAAAAT
Found at i:62249 original size:26 final size:26
Alignment explanation
Indices: 62220--62270 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
62210 TAGAAGTACA
*
62220 TAATTTTAG-TTTCTTATTCTACAAGT
1 TAATTTTAGCTTT-TTAGTCTACAAGT
62246 TAATTTTAGCTTTTTAGTCTACAAG
1 TAATTTTAGCTTTTTAGTCTACAAG
62271 AATAAAGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (26 bp):
TAATTTTAGCTTTTTAGTCTACAAGT
Found at i:67458 original size:102 final size:102
Alignment explanation
Indices: 67330--67520 Score: 249
Period size: 102 Copynumber: 1.9 Consensus size: 102
67320 CCGGTTTCAC
* * * * * * *
67330 TATCATATAATTTCTTTAAATTATTAAGCTAGAATTCTTTTCATTTTCAAAGAGATACAGAAGCA
1 TATCATATAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAAAGAGATACAGAAGCA
*
67395 TCA-ATACGGCAAAATGGCAAGAACATGACTGTTGGTT
66 T-ATATACGGCAAAATGACAAGAACATGACTGTTGGTT
* * * *
67432 TATCATCTAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAATGAGATACAGATGTA
1 TATCATATAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAAAGAGATACAGAAGCA
*
67497 TATATACGGCTAAATGACAAGAAC
66 TATATACGGCAAAATGACAAGAAC
67521 GTTCATGTAG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
101 1 0.01
102 74 0.99
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (102 bp):
TATCATATAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAAAGAGATACAGAAGCA
TATATACGGCAAAATGACAAGAACATGACTGTTGGTT
Found at i:70125 original size:3 final size:3
Alignment explanation
Indices: 70117--70152 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
70107 TCTAATGTTG
70117 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
70153 GCATTTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.