Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002741.1 Kokia drynarioides strain JFW-HI SEQ_115047, 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: 29014
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:970 original size:24 final size:26
Alignment explanation
Indices: 943--990 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
933 AGAGAAATGT
943 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGATATTATGAG
967 AAATGATGAATATGAGATATTATG
1 AAATGATGAATATGAGATATTATG
991 CCCATATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (26 bp):
AAATGATGAATATGAGATATTATGAG
Found at i:3527 original size:31 final size:31
Alignment explanation
Indices: 3481--3560 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
3471 TGTCTTTCTT
*
3481 AAACTTT-T-AATGCATGAAAATGCAATGCA
1 AAACTTTATGAATGCATGAAAATACAATGCA
** *
3510 AAACTTTATGAATGCATGAAAATATGATGCG
1 AAACTTTATGAATGCATGAAAATACAATGCA
*
3541 AAATTTTATGAATGCATGAA
1 AAACTTTATGAATGCATGAA
3561 TGCATATGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 7 0.16
30 1 0.02
31 36 0.82
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATACAATGCA
Found at i:6149 original size:15 final size:15
Alignment explanation
Indices: 6129--6174 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
6119 ACATTCATAA
6129 AAATAATAAATAAAT
1 AAATAATAAATAAAT
6144 AAATAA-AAATAAA-
1 AAATAATAAATAAAT
6157 ATAA-AATAAAATAAAT
1 A-AATAAT-AAATAAAT
6173 AA
1 AA
6175 TTAGCTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.11
14 9 0.33
15 14 0.52
16 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:6151 original size:21 final size:24
Alignment explanation
Indices: 6125--6174 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
6115 ATTTACATTC
6125 ATAAAAAT-AAT-AAAT-AAATAA
1 ATAAAAATAAATAAAATAAAATAA
6146 ATAAAAATAAAATAAAATAAAATAA
1 ATAAAAAT-AAATAAAATAAAATAA
6171 ATAA
1 ATAA
6175 TTAGCTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
23 3 0.12
24 4 0.16
25 10 0.40
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (24 bp):
ATAAAAATAAATAAAATAAAATAA
Found at i:7324 original size:20 final size:19
Alignment explanation
Indices: 7253--7326 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
7243 ACTAATTCGA
7253 AGAAATACCAAAAAATATG
1 AGAAATACCAAAAAATATG
* *
7272 AGATATACCAAAAATTATG
1 AGAAATACCAAAAAATATG
* * **
7291 AAAAAAGAGTAAAAAATATG
1 -AGAAATACCAAAAAATATG
*
7311 AGGAAACACCAAAAAA
1 A-GAAATACCAAAAAA
7327 AACATGAAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
19 18 0.44
20 23 0.56
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (19 bp):
AGAAATACCAAAAAATATG
Found at i:7690 original size:20 final size:20
Alignment explanation
Indices: 7607--7691 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
7597 AAAGTATCAA
*
7607 AAAAAATATGAAGATATACG
1 AAAAAATATGAAGATATACT
*
7627 AAAAATTATGAAGGA-ATA-T
1 AAAAAATATGAA-GATATACT
* * *
7646 AAAAAA-ACTGAGGATGTATCA
1 AAAAAATA-TGAAGATATA-CT
7667 AAAAAATATGAGAGA-ATACT
1 AAAAAATATGA-AGATATACT
7687 AAAAA
1 AAAAA
7692 TTTTAAGGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
18 3 0.06
19 10 0.20
20 20 0.41
21 13 0.27
22 3 0.06
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (20 bp):
AAAAAATATGAAGATATACT
Found at i:9570 original size:39 final size:42
Alignment explanation
Indices: 9520--9658 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 42
9510 TTTTGCTATT
* *
9520 TCAGGGCCAAAGAGGAAAAT-A-GA-AGATTCTTGTGATATT
1 TCAGGGGCAAAGAGGAAAATAAGGACAGATTCTTGTGATATC
* *
9559 TCAGGGGCAAAG-CGAAAATCAGAGGACAGATTCTTGTGATGTC
1 TCAGGGGCAAAGAGGAAAAT-A-AGGACAGATTCTTGTGATATC
* * *
9602 TCTGGGGAAAAGA-GAAAATCAGAGGACAGATTCTTGTGATGTC
1 TCAGGGGCAAAGAGGAAAAT-A-AGGACAGATTCTTGTGATATC
*
9645 TCTGGGGCAAAGAG
1 TCAGGGGCAAAGAG
9659 AAAGATTCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
38 6 0.07
39 11 0.13
41 1 0.01
42 2 0.02
43 66 0.77
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (42 bp):
TCAGGGGCAAAGAGGAAAATAAGGACAGATTCTTGTGATATC
Found at i:9619 original size:43 final size:43
Alignment explanation
Indices: 9543--9661 Score: 193
Period size: 43 Copynumber: 2.8 Consensus size: 43
9533 GGAAAATAGA
* * * *
9543 AGATTCTTGTGATATTTCAGGGGCAAAGCGAAAATCAGAGGAC
1 AGATTCTTGTGATGTCTCTGGGGCAAAGAGAAAATCAGAGGAC
*
9586 AGATTCTTGTGATGTCTCTGGGGAAAAGAGAAAATCAGAGGAC
1 AGATTCTTGTGATGTCTCTGGGGCAAAGAGAAAATCAGAGGAC
9629 AGATTCTTGTGATGTCTCTGGGGCAAAGAGAAA
1 AGATTCTTGTGATGTCTCTGGGGCAAAGAGAAA
9662 GATTCCTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (43 bp):
AGATTCTTGTGATGTCTCTGGGGCAAAGAGAAAATCAGAGGAC
Found at i:11447 original size:18 final size:18
Alignment explanation
Indices: 11424--11470 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
11414 GACATTCTCG
**
11424 AATTATATTTTTATTTTA
1 AATTATATTTAAATTTTA
*
11442 AATTATCTTTAAATTTTA
1 AATTATATTTAAATTTTA
*
11460 AAATA-ATTTAA
1 AATTATATTTAA
11471 TTACATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTATATTTAAATTTTA
Found at i:11610 original size:7 final size:7
Alignment explanation
Indices: 11598--11623 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11588 CATAGTTTTT
11598 AAAATTA
1 AAAATTA
11605 AAAATTA
1 AAAATTA
11612 AAAATTA
1 AAAATTA
11619 AAAAT
1 AAAAT
11624 ACAGTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:14386 original size:39 final size:39
Alignment explanation
Indices: 14340--14555 Score: 204
Period size: 39 Copynumber: 5.5 Consensus size: 39
14330 AGAAGAGACC
* * * * *
14340 TCTGATTTTCCCTTTGGCCCTGATAAATTACAGGAATCT
1 TCTGATTTTCTCTTTGCCCCTGAGAAATCACAAGAATCT
* ** * * *
14379 TCAGATTTTCTCTTTGGTCCTGAGGAA-CTAGAGGAATCT
1 TCTGATTTTCTCTTTGCCCCTGAGAAATC-ACAAGAATCT
* * * *
14418 TCGGATTTTCTCTTTACCCCAGAGACATCACAAGAATCT
1 TCTGATTTTCTCTTTGCCCCTGAGAAATCACAAGAATCT
* *
14457 TCTGATTTTCTCTTTGCCCCAGAGACATCACAAGAATCT
1 TCTGATTTTCTCTTTGCCCCTGAGAAATCACAAGAATCT
* *
14496 TCTGATTTTCGCTTTGCCCCTGA-AATATCATAAGAATCT
1 TCTGATTTTCTCTTTGCCCCTGAGAA-ATCACAAGAATCT
*
14535 TCT-ATTTTCCTCTTTGGCCCT
1 TCTGATTTT-CTCTTTGCCCCT
14556 AAAATAGCAA
Statistics
Matches: 149, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
38 6 0.04
39 142 0.95
40 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (39 bp):
TCTGATTTTCTCTTTGCCCCTGAGAAATCACAAGAATCT
Found at i:17674 original size:21 final size:21
Alignment explanation
Indices: 17650--17690 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17640 ACAAAACCTC
*
17650 ATTTTGTCCTCTAGAAACACA
1 ATTTTATCCTCTAGAAACACA
*
17671 ATTTTATTCTCTAGAAACAC
1 ATTTTATCCTCTAGAAACAC
17691 TATATTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (21 bp):
ATTTTATCCTCTAGAAACACA
Found at i:22401 original size:19 final size:20
Alignment explanation
Indices: 22364--22402 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
22354 TTATTACTGA
*
22364 ATATTTATAAATTGTAATAT
1 ATATTTATAAATTGAAATAT
*
22384 ATATTTAT-TATTGAAATAT
1 ATATTTATAAATTGAAATAT
22403 TAATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATTTATAAATTGAAATAT
Found at i:22521 original size:18 final size:17
Alignment explanation
Indices: 22487--22521 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
22477 ATTTTTAAAA
*
22487 TTTTATTTTAATTTAAT
1 TTTTATTTTAATATAAT
22504 TTTTATTCTTAATATAAT
1 TTTTATT-TTAATATAAT
22522 AATATTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTTTAATATAAT
Found at i:24401 original size:65 final size:64
Alignment explanation
Indices: 24292--24434 Score: 153
Period size: 65 Copynumber: 2.2 Consensus size: 64
24282 TATCAATGTT
* * * *
24292 TTTAAATA-TTTCTCATACATATTTACAATCTAATTTTCAGTTTCTTGATGAATTACATACACA
1 TTTAAATATTTTCACATACATATTTACAATCTAATTTTCAATTTCTTAATAAATTACATACACA
* * * * * *
24355 TTTAAATATTTTTCACATATATATTTATAGTCTAATTTTTAATTTCTTAATAAATTATATATACA
1 TTTAAATA-TTTTCACATACATATTTACAATCTAATTTTCAATTTCTTAATAAATTACATACACA
**
24420 TGCAAATATATTTCA
1 TTTAAATAT-TTTCA
24435 ATTACATTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 8 0.12
64 1 0.02
65 56 0.86
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (64 bp):
TTTAAATATTTTCACATACATATTTACAATCTAATTTTCAATTTCTTAATAAATTACATACACA
Found at i:24753 original size:69 final size:69
Alignment explanation
Indices: 24642--24786 Score: 281
Period size: 69 Copynumber: 2.1 Consensus size: 69
24632 CCAAAACAGG
24642 CCTAAATAAGCGAAACACACCAAAATTTTGACCGGAACTGAACATAGACTACACGGTACCAGCTT
1 CCTAAATAAGCGAAACACACCAAAATTTTGACCGGAACTGAACATAGACTACACGGTACCAGCTT
24707 AAGA
66 AAGA
24711 CCTAAATAAGCGAAACACACCAAAATTTTGACCGGAACTGAACATAGACTACACGGTACCAGCTT
1 CCTAAATAAGCGAAACACACCAAAATTTTGACCGGAACTGAACATAGACTACACGGTACCAGCTT
24776 AAGA
66 AAGA
*
24780 CCGAAAT
1 CCTAAAT
24787 GATATGTACT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.17
Consensus pattern (69 bp):
CCTAAATAAGCGAAACACACCAAAATTTTGACCGGAACTGAACATAGACTACACGGTACCAGCTT
AAGA
Found at i:27163 original size:12 final size:12
Alignment explanation
Indices: 27146--27173 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27136 GATATTTGAT
27146 CTTCTTTAAAAA
1 CTTCTTTAAAAA
27158 CTTCTTTAAAAA
1 CTTCTTTAAAAA
27170 CTTC
1 CTTC
27174 GGTACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (12 bp):
CTTCTTTAAAAA
Done.