Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002852.1 Kokia drynarioides strain JFW-HI SEQ_115244, 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: 12712
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:630 original size:19 final size:17
Alignment explanation
Indices: 608--650 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
598 TATATTTTGT
608 TTTTACTTTAGCATTTATA
1 TTTTA-TTTAGCATTT-TA
* *
627 TTTTATTTATCCTTTTA
1 TTTTATTTAGCATTTTA
644 TTTTATT
1 TTTTATT
651 ACCATACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 8 0.36
19 5 0.23
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATTTAGCATTTTA
Found at i:2555 original size:21 final size:21
Alignment explanation
Indices: 2531--2571 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2521 TTACATTTTC
*
2531 TAAAGTTAAAA-GTAAAACTAT
1 TAAA-TTAAAAGGCAAAACTAT
2552 TAAATTAAAAGGCAAAACTA
1 TAAATTAAAAGGCAAAACTA
2572 CATCATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24
Consensus pattern (21 bp):
TAAATTAAAAGGCAAAACTAT
Found at i:5052 original size:3 final size:3
Alignment explanation
Indices: 5044--5075 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5034 ATTAAATGGT
5044 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5076 GTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6175 original size:29 final size:29
Alignment explanation
Indices: 6122--6371 Score: 206
Period size: 29 Copynumber: 8.5 Consensus size: 29
6112 TAAATTGTCT
* *
6122 AAAAATTACATTTTT-ACCCCCCGAACTTTC
1 AAAAATTCCATTTTTGA--CCCCGAACTTCC
* **
6152 AAAAATTCCATTTTTGACCTCGAAACTTTT
1 AAAAATTCCATTTTTGACCCCG-AACTTCC
* * *
6182 GAAAA-T-CATATTTTTACACTCGAACTTCC
1 AAAAATTCCAT-TTTTGAC-CCCGAACTTCC
6211 AAAAATTCCATTTTT-ACCCCCGAACTTCC
1 AAAAATTCCATTTTTGA-CCCCGAACTTCC
6240 AAAAATTCCATTTTTGACCCCGAAACTTCC
1 AAAAATTCCATTTTTGACCCCG-AACTTCC
* ** **
6270 AAAAATTCCATTTTTAACCCTAAAACTTTT
1 AAAAATTCCATTTTTGACCC-CGAACTTCC
* *
6300 GAAAA-TCACATTTTT-ACCCCTAAACTTCC
1 AAAAATTC-CATTTTTGACCCC-GAACTTCC
* * *
6329 AAAAATTCCATTTTTGACACCAAACCTCC
1 AAAAATTCCATTTTTGACCCCGAACTTCC
6358 AAAAATTCCATTTT
1 AAAAATTCCATTTT
6372 CAACCCTAAA
Statistics
Matches: 185, Mismatches: 21, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
28 3 0.02
29 95 0.51
30 83 0.45
31 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTGACCCCGAACTTCC
Found at i:6215 original size:59 final size:57
Alignment explanation
Indices: 6131--6346 Score: 222
Period size: 59 Copynumber: 3.6 Consensus size: 57
6121 TAAAAATTAC
*
6131 ATTTTTACCCCCCGAACTTTCAAAAATTCCATTTTTGACCTCGAAACTTTTGAAAATCAT
1 ATTTTTA--CCCCGAACTTCCAAAAATTCCATTTTTGACC-CGAAACTTTTGAAAATCAT
* ***
6191 ATTTTTACACTCGAACTTCCAAAAATTCCATTTTT-ACCCCCG-AACTTCCAAAAATTCCAT
1 ATTTTTAC-CCCGAACTTCCAAAAATTCCATTTTTGA--CCCGAAACTTTTGAAAA-T-CAT
* * * *
6251 -TTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTTGAAAATCAC
1 ATTTTTACCCCG-AACTTCCAAAAATTCCATTTTTGACCC-GAAACTTTTGAAAATCAT
*
6309 ATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGAC
1 ATTTTTACCCC-GAACTTCCAAAAATTCCATTTTTGAC
6347 ACCAAACCTC
Statistics
Matches: 130, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
58 19 0.15
59 89 0.68
60 22 0.17
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (57 bp):
ATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCCGAAACTTTTGAAAATCAT
Found at i:6274 original size:118 final size:117
Alignment explanation
Indices: 6122--6371 Score: 328
Period size: 118 Copynumber: 2.1 Consensus size: 117
6112 TAAATTGTCT
* * * *
6122 AAAAATTACATTTTTACCCCCCGAACTTTCAAAAATTCCATTTTTGA-CCTCGAAACTTTTGAAA
1 AAAAATTCCATTTTTA-CCCCCGAACTTCCAAAAATTCCATTTTTAACCCT-AAAACTTTTGAAA
* * * * * *
6186 ATCATATTTTTA-CACTCGAACTTCCAAAAATTCCATTTTT-ACCCCCGAACTTCC
64 ATCACATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGA-CACCAAACCTCC
6240 AAAAATTCCATTTTTGA-CCCCGAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTTGAAA
1 AAAAATTCCATTTTT-ACCCCCG-AACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTTGAAA
6304 ATCACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACACCAAACCTCC
64 ATCACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACACCAAACCTCC
6358 AAAAATTCCATTTT
1 AAAAATTCCATTTT
6372 CAACCCTAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
117 5 0.04
118 104 0.89
119 8 0.07
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (117 bp):
AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTTGAAAAT
CACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACACCAAACCTCC
Found at i:6391 original size:29 final size:29
Alignment explanation
Indices: 6204--6394 Score: 156
Period size: 30 Copynumber: 6.4 Consensus size: 29
6194 TTTACACTCG
***
6204 AACTTCCAAAAATTCCATTTTT-ACCCCCG
1 AACTT-CAAAAATTCCATTTTTAACCCTAA
* **
6233 AACTTCCAAAAATTCCATTTTTGACCCCGA
1 AACTT-CAAAAATTCCATTTTTAACCCTAA
6263 AACTTCCAAAAATTCCATTTTTAACCCTAA
1 AACTT-CAAAAATTCCATTTTTAACCCTAA
** *
6293 AACTTTTGAAAA-TCACATTTTTACCCCT-A
1 AAC-TTCAAAAATTC-CATTTTTAACCCTAA
*
6322 AACTTCCAAAAATTCCATTTTTGACACC-AA
1 AACTT-CAAAAATTCCATTTTTAAC-CCTAA
* * *
6352 ACCTCCAAAAATTCCATTTTCAACCCTAA
1 AACTTCAAAAATTCCATTTTTAACCCTAA
*
6381 AACTTTTAAAAATT
1 AAC-TTCAAAAATT
6395 AGCACTTTGC
Statistics
Matches: 134, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
28 4 0.03
29 61 0.46
30 67 0.50
31 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCAAAAATTCCATTTTTAACCCTAA
Found at i:6394 original size:59 final size:56
Alignment explanation
Indices: 6204--6381 Score: 187
Period size: 59 Copynumber: 3.0 Consensus size: 56
6194 TTTACACTCG
* * *
6204 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTTA--CCCAAACTTCCAAAAATTCCATTTTT-AACCCTA
*** *
6263 AACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTTGAAAA-TCACATTTTTACCCCTA
1 AACTTCCAAAAATTCCATTTTT-ACCC--AAACTTCCAAAAATTC-CATTTTTAACCCTA
* *
6322 AACTTCCAAAAATTCCATTTTTGACACCAAACCTCCAAAAATTCCATTTTCAACCCTA
1 AACTTCCAAAAATTCCATTTTT-AC-CCAAACTTCCAAAAATTCCATTTTTAACCCTA
6380 AA
1 AA
6382 ACTTTTAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
58 26 0.26
59 56 0.55
60 19 0.19
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (56 bp):
AACTTCCAAAAATTCCATTTTTACCCAAACTTCCAAAAATTCCATTTTTAACCCTA
Found at i:7895 original size:18 final size:16
Alignment explanation
Indices: 7872--7910 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
7862 CATAAGTATA
7872 AATATTTATATTAAATAT
1 AATATTTATA-TAAA-AT
*
7890 AATATTTGTATAAAAT
1 AATATTTATATAAAAT
7906 AATAT
1 AATAT
7911 AAATAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
AATATTTATATAAAAT
Found at i:11147 original size:77 final size:76
Alignment explanation
Indices: 10958--11447 Score: 265
Period size: 77 Copynumber: 6.2 Consensus size: 76
10948 GAAACTAAAT
* * * *
10958 CAAAATCAAATCAAATCAGTTGAATGGCGAGAATAAATCTCGAAACATAATTATTTAATTTTAAT
1 CAAAATCAAATAAAATCAGTTGAACGGCGAGAATAAATCTCGAAACAAAATTATTCAA--TTAAT
* **
11023 TCTTGTTTGGTAA
64 TCTTATTTGAAAA
* * *
11036 CGAAATCAGAATAAAACCAGTTGAACGACGAGAATAAATCTCGAAACAAAATTATTCAATTAATT
1 CAAAATCA-AATAAAATCAGTTGAACGGCGAGAATAAATCTCGAAACAAAATTATTCAATTAATT
11101 CTTATTTGAAAA
65 CTTATTTGAAAA
* * * * * * *
11113 CAAAATCCAAATTAATTCTGTTGAACGGCAAGAATAAA-CACCGAAATAGAATTATTCAATTAAT
1 CAAAAT-CAAATAAAATCAGTTGAACGGCGAGAATAAATC-TCGAAACAAAATTATTCAATTAAT
* *
11177 TATTA-TT-AAAT
64 TCTTATTTGAAAA
* * * * * ** * * * *
11188 TAAAATATAGAAGAAAATCTGTTAAACAACGGGAATAAATC-CTGAAACAGATTTATTTAACTT-
1 CAAAAT-CA-AATAAAATCAGTTGAACGGCGAGAATAAATCTC-GAAACAAAATTATTCAA-TTA
* *
11251 ATTCTTGTTTTGGAAA
62 ATTCTT-ATTTGAAAA
* * * ** * *
11267 CAAAATTAAAATAAAATAAAATCGATTAAACAACGAGAATAAATCTCGAAATAAAATTATTCACT
1 CAAAA-TCAAATAAAAT--CA--G-TTGAACGGCGAGAATAAATCTCGAAACAAAATTATTCAAT
* *
11332 TAATTCTTAATTGGAAA
60 TAATTCTTATTTGAAAA
* * * * *
11349 CAAAATTAAAATAGAATAAAAT-ATATTAAATGGCGAGAATAAATCTCGAAACAGAATTATT-AA
1 CAAAA-T----CA-AATAAAATCA-GTTGAACGGCGAGAATAAATCTCGAAACAAAATTATTCAA
* *
11412 CTTAATTCTTAATTGGAAA
59 -TTAATTCTTATTTGAAAA
*
11431 CAAAATAAAAATAAAAT
1 CAAAAT-CAAATAAAAT
11448 AAAATCTATT
Statistics
Matches: 325, Mismatches: 63, Indels: 49
0.74 0.14 0.11
Matches are distributed among these distances:
75 10 0.03
76 43 0.13
77 79 0.24
78 20 0.06
79 51 0.16
80 1 0.00
81 2 0.01
82 71 0.22
83 37 0.11
84 2 0.01
86 1 0.00
87 8 0.02
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (76 bp):
CAAAATCAAATAAAATCAGTTGAACGGCGAGAATAAATCTCGAAACAAAATTATTCAATTAATTC
TTATTTGAAAA
Found at i:11377 original size:82 final size:82
Alignment explanation
Indices: 11184--11491 Score: 377
Period size: 82 Copynumber: 3.7 Consensus size: 82
11174 AATTATTATT
* * * *
11184 AAATTAAAATATAGAAGAAAATCTGTTAAACAACGGGAATAAATC-CTGAAACAGATTTATTTAA
1 AAATTAAAATA-A-AATAAAATCTATTAAACAACGAGAATAAATCTC-GAAACAGAATTA-TTAA
**
11248 CTT-ATTCTTGTTTTGGAAACA
62 CTTAATTCTT-AATTGGAAACA
* * * *
11269 AAATTAAAATAAAATAAAATCGATTAAACAACGAGAATAAATCTCGAAATAAAATTATTCACTTA
1 AAATTAAAATAAAATAAAATCTATTAAACAACGAGAATAAATCTCGAAACAGAATTATTAACTTA
11334 ATTCTTAATTGGAAACA
66 ATTCTTAATTGGAAACA
* * ***
11351 AAATTAAAATAGAATAAAATATATTAAATGGCGAGAATAAATCTCGAAACAGAATTATTAACTTA
1 AAATTAAAATAAAATAAAATCTATTAAACAACGAGAATAAATCTCGAAACAGAATTATTAACTTA
11416 ATTCTTAATTGGAAACA
66 ATTCTTAATTGGAAACA
* * * * *
11433 AAATAAAAATAAAATAAAATCTATTGAACGACGAGAATAAATCTCGAAAAAGATTTATT
1 AAATTAAAATAAAATAAAATCTATTAAACAACGAGAATAAATCTCGAAACAGAATTATT
11492 CGGTTTTAAT
Statistics
Matches: 194, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
82 139 0.72
83 42 0.22
84 2 0.01
85 11 0.06
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (82 bp):
AAATTAAAATAAAATAAAATCTATTAAACAACGAGAATAAATCTCGAAACAGAATTATTAACTTA
ATTCTTAATTGGAAACA
Found at i:12643 original size:62 final size:62
Alignment explanation
Indices: 12561--12688 Score: 249
Period size: 62 Copynumber: 2.1 Consensus size: 62
12551 ATTAAATGAG
12561 ATAT-TTTAAGTGAGACTTCTAGAGAATTTGAGAAAGGTTAAAAATCAATTAAAAGTTAAAA
1 ATATCTTTAAGTGAGACTTCTAGAGAATTTGAGAAAGGTTAAAAATCAATTAAAAGTTAAAA
12622 ATATCTTTAAGTGAGACTTCTAGAGAATTTGAGAAAGGTTAAAAATCAATTAAAAGTTAAAA
1 ATATCTTTAAGTGAGACTTCTAGAGAATTTGAGAAAGGTTAAAAATCAATTAAAAGTTAAAA
12684 ATATC
1 ATATC
12689 AGCTCTTTTC
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
61 4 0.06
62 62 0.94
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (62 bp):
ATATCTTTAAGTGAGACTTCTAGAGAATTTGAGAAAGGTTAAAAATCAATTAAAAGTTAAAA
Done.