Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013931.1 Kokia drynarioides strain JFW-HI SEQ_128961, 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: 37431
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1149 original size:59 final size:58
Alignment explanation
Indices: 1065--1216 Score: 173
Period size: 59 Copynumber: 2.6 Consensus size: 58
1055 TAAACTTAAT
* * *
1065 ACTTTTTCTTAATTTGGTACTTTAACTTTTTTTGACCT-ATTTTGGCATTTGAACTTGA
1 ACTTTTTCCTAATTTGGTAC-TTAACTTTTTTTGACCTCAATTTGGCACTTGAACTTGA
* *
1123 CACTTTTTCCTAATTTGGTATCTTAAC-TTTTTTGAGCTCAATTTGGTACTTGAACTTGA
1 -ACTTTTTCCTAATTTGGTA-CTTAACTTTTTTTGACCTCAATTTGGCACTTGAACTTGA
* *
1182 ATTTTTTCCCATAATTTGGTACCTAATCTTTTTTT
1 ACTTTTT-CC-TAATTTGGTACTTAA-CTTTTTTT
1217 TTTAAGATTC
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
58 16 0.20
59 46 0.57
60 12 0.15
61 6 0.08
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.52
Consensus pattern (58 bp):
ACTTTTTCCTAATTTGGTACTTAACTTTTTTTGACCTCAATTTGGCACTTGAACTTGA
Found at i:1510 original size:28 final size:26
Alignment explanation
Indices: 1434--1522 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 26
1424 TTCGGATCTC
* *
1434 AAAAAGTTTAAGTAACAACTTAAAAA
1 AAAAAGTTTAAGTACCAAATTAAAAA
1460 AAAGTGTCAAGTTTAAGTACCAAATTAGACAAA
1 AAA-----AAGTTTAAGTACCAAATTA-A-AAA
*
1493 AAAAAGTTTAAGTGCCAAATTAAAAA
1 AAAAAGTTTAAGTACCAAATTAAAAA
1519 AAAA
1 AAAA
1523 TATCAAATTC
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
26 10 0.19
27 1 0.02
28 18 0.34
31 17 0.32
32 1 0.02
33 6 0.11
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.22
Consensus pattern (26 bp):
AAAAAGTTTAAGTACCAAATTAAAAA
Found at i:16544 original size:20 final size:20
Alignment explanation
Indices: 16519--16583 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
16509 TAGAGACATC
*
16519 GAAGTGCAAACAAAGGTACT
1 GAAGTGCAAACAAAGGCACT
* * * *
16539 GAAGTGTAAATAAAGACACC
1 GAAGTGCAAACAAAGGCACT
16559 GAAGTGCAAACAAAGGCACT
1 GAAGTGCAAACAAAGGCACT
16579 GAAGT
1 GAAGT
16584 ATAATCCCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.14
Consensus pattern (20 bp):
GAAGTGCAAACAAAGGCACT
Found at i:16580 original size:40 final size:40
Alignment explanation
Indices: 16475--16583 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
16465 CGTTCAGAGG
* * * * * *
16475 CACCGTAGTTCAAACAAAGACACTAAAATGTAAATAGAGA
1 CACCGAAGTGCAAACAAAGGCACTGAAGTGTAAATAAAGA
* *
16515 CATCGAAGTGCAAACAAAGGTACTGAAGTGTAAATAAAGA
1 CACCGAAGTGCAAACAAAGGCACTGAAGTGTAAATAAAGA
16555 CACCGAAGTGCAAACAAAGGCACTGAAGT
1 CACCGAAGTGCAAACAAAGGCACTGAAGT
16584 ATAATCCCAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (40 bp):
CACCGAAGTGCAAACAAAGGCACTGAAGTGTAAATAAAGA
Found at i:19046 original size:22 final size:22
Alignment explanation
Indices: 19020--19061 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19010 TATGTATAGG
*
19020 TCATTGTATCTCAAGACTTGTA
1 TCATTATATCTCAAGACTTGTA
*
19042 TCATTATGTCTCAAGACTTG
1 TCATTATATCTCAAGACTTG
19062 CTTGGTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (22 bp):
TCATTATATCTCAAGACTTGTA
Found at i:19955 original size:14 final size:15
Alignment explanation
Indices: 19934--19965 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19924 GTTAATTTTT
19934 TTGAAAAAATTCTGG
1 TTGAAAAAATTCTGG
19949 TTGAAAAAATTCTGG
1 TTGAAAAAATTCTGG
19964 TT
1 TT
19966 CGGTTAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (15 bp):
TTGAAAAAATTCTGG
Found at i:20604 original size:12 final size:12
Alignment explanation
Indices: 20587--20612 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20577 CATTGGGGGA
20587 GAGCTCAATCAC
1 GAGCTCAATCAC
20599 GAGCTCAATCAC
1 GAGCTCAATCAC
20611 GA
1 GA
20613 TACTATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (12 bp):
GAGCTCAATCAC
Found at i:22390 original size:80 final size:80
Alignment explanation
Indices: 22282--22465 Score: 251
Period size: 80 Copynumber: 2.3 Consensus size: 80
22272 ATGACTGTAA
* ** * *
22282 GGACCTCTACGATGACTAAGATTCTGCATATGTTGTAGTTTCTTGACAACTTCTGTGAGCAACAT
1 GGACC-CTACGATGGCTGGGATTCTGCATATGTTGTAGTTTCTTAACAACTTCTGTAAGCAACAT
22347 CGTGAGTGGGAAACAT
65 CGTGAGTGGGAAACAT
* *
22363 GGACCCTACGATGGCTGGGATTCTGCATATGTTGTAGTTTCTTAACAACTTGTGTAAGCAGCATC
1 GGACCCTACGATGGCTGGGATTCTGCATATGTTGTAGTTTCTTAACAACTTCTGTAAGCAACATC
* *
22428 GTGAGTGGGTAATAT
66 GTGAGTGGGAAACAT
**
22443 GGACTGTACCGATGGCTGGGATT
1 GGACCCTA-CGATGGCTGGGATT
22466 GTATAAATGT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
80 72 0.79
81 19 0.21
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (80 bp):
GGACCCTACGATGGCTGGGATTCTGCATATGTTGTAGTTTCTTAACAACTTCTGTAAGCAACATC
GTGAGTGGGAAACAT
Found at i:22498 original size:81 final size:80
Alignment explanation
Indices: 22282--22486 Score: 203
Period size: 80 Copynumber: 2.5 Consensus size: 80
22272 ATGACTGTAA
* ** * * * * * * *
22282 GGACCTCTACGATGACTAAGATTCTGCATATGTTGTAGTTTCTTGACAACTTCTGTGAGCAACAT
1 GGACC-CTACGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAGCAACAT
22347 CGTGAGTGGGAAACAT
65 CGTGAGTGGGAAACAT
* * * * *
22363 GGACCCTACGATGGCTGGGATTCTGCATATGTTGTAGTTTCTTAACAACTTGTGTAAGCAGCATC
1 GGACCCTACGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAGCAACATC
* *
22428 GTGAGTGGGTAATAT
66 GTGAGTGGGAAACAT
** * *
22443 GGACTGTACCGATGGCTGGGATTGTATAAATGTTATAGTTTCCT
1 GGACCCTA-CGATGGCTGGGATTCTACAAATGTTATAGTTTCCT
22487 NATAGCTTGT
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
80 72 0.68
81 34 0.32
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (80 bp):
GGACCCTACGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAGCAACATC
GTGAGTGGGAAACAT
Found at i:22510 original size:81 final size:80
Alignment explanation
Indices: 22282--22511 Score: 192
Period size: 80 Copynumber: 2.9 Consensus size: 80
22272 ATGACTGTAA
* ** * * * * * * *
22282 GGACCTCTACGATGACTAAGATTCTGCATATGTTGTAGTTTCTTGACAACTTCTGTGAGCAA-CA
1 GGACC-CTACGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAG-AAGCA
22346 TCGTGAGTGGGAAACAT
64 TCGTGAGTGGGAAACAT
* * * * *
22363 GGACCCTACGATGGCTGGGATTCTGCATATGTTGTAGTTTCTTAACAACTTGTGTAAGCAGCATC
1 GGACCCTACGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAGAAGCATC
* *
22428 GTGAGTGGGTAATAT
66 GTGAGTGGGAAACAT
** * * * * * * *
22443 GGACTGTACCGATGGCTGGGATTGTATAAATGTTATAGTTTCCTNATAGCTTGTGTTAGAAGTAT
1 GGACCCTA-CGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAGAAGCAT
22508 CGTG
65 CGTG
22512 TACTGGTTAA
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
79 1 0.01
80 70 0.56
81 53 0.43
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (80 bp):
GGACCCTACGATGGCTGGGATTCTACAAATGTTATAGTTTCCTAACAACTTGTGTAAGAAGCATC
GTGAGTGGGAAACAT
Found at i:23724 original size:36 final size:36
Alignment explanation
Indices: 23675--23896 Score: 135
Period size: 36 Copynumber: 6.2 Consensus size: 36
23665 ATGGCCTTAT
* *
23675 GCTCTAATTGAGACATAAG-AGATCA-CTTAGCATTAC
1 GCTCTAATCGAGACATAAGCA-A-CATCTTAGCAATAC
* *
23711 GCTCTAATCGAGACCTATGCAACATCTTAGCAATAC
1 GCTCTAATCGAGACATAAGCAACATCTTAGCAATAC
* * * * *
23747 GCTCTAACCGAGACGTATGCAACATCATAGCAATAT
1 GCTCTAATCGAGACATAAGCAACATCTTAGCAATAC
* * * * **
23783 GCTCTAACCAAGACGTTA-CAACATGATAGCAATAC
1 GCTCTAATCGAGACATAAGCAACATCTTAGCAATAC
* * * ** *
23818 ACTTTAACCGAGATGTATGCAACATCTTAGCAATAC
1 GCTCTAATCGAGACATAAGCAACATCTTAGCAATAC
* * * * * * * * *
23854 ACTCTAACCAAGACGTATGTAACATCATAGTAATAT
1 GCTCTAATCGAGACATAAGCAACATCTTAGCAATAC
23890 GCTCTAA
1 GCTCTAA
23897 CCGAAATGTA
Statistics
Matches: 154, Mismatches: 29, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
35 29 0.19
36 124 0.81
37 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (36 bp):
GCTCTAATCGAGACATAAGCAACATCTTAGCAATAC
Found at i:23826 original size:71 final size:71
Alignment explanation
Indices: 23738--23869 Score: 210
Period size: 71 Copynumber: 1.9 Consensus size: 71
23728 TGCAACATCT
* **
23738 TAGCAATACGCTCTAACCGAGACGTATGCAACATCATAGCAATATGCTCTAACCAAGACGTTACA
1 TAGCAATACACTCTAACCGAGACGTATGCAACATCATAGCAATACACTCTAACCAAGACGTTACA
23803 ACATGA
66 ACATGA
* * *
23809 TAGCAATACACTTTAACCGAGATGTATGCAACATCTTAGCAATACACTCTAACCAAGACGT
1 TAGCAATACACTCTAACCGAGACGTATGCAACATCATAGCAATACACTCTAACCAAGACGT
23870 ATGTAACATC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (71 bp):
TAGCAATACACTCTAACCGAGACGTATGCAACATCATAGCAATACACTCTAACCAAGACGTTACA
ACATGA
Found at i:23897 original size:36 final size:36
Alignment explanation
Indices: 23702--23909 Score: 238
Period size: 36 Copynumber: 5.8 Consensus size: 36
23692 AGAGATCACT
* * * *
23702 TAGCATTACGCTCTAATCGAGACCTATGCAACATCT
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
23738 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
* * * *
23774 TAGCAATATGCTCTAACCAAGACGT-TACAACATGA
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
* * * *
23809 TAGCAATACACTTTAACCGAGATGTATGCAACATCT
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
* * *
23845 TAGCAATACACTCTAACCAAGACGTATGTAACATCA
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
* * * *
23881 TAGTAATATGCTCTAACCGAAATGTATGC
1 TAGCAATACGCTCTAACCGAGACGTATGC
23910 TTTCCTTTGA
Statistics
Matches: 143, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 28 0.20
36 115 0.80
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (36 bp):
TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
Found at i:29812 original size:21 final size:21
Alignment explanation
Indices: 29788--29837 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
29778 CAACTTAAAG
29788 CGGAGGCAGCAACGAGGGAAA
1 CGGAGGCAGCAACGAGGGAAA
* *
29809 CGGAGGTAGCAACGAGGGAAG
1 CGGAGGCAGCAACGAGGGAAA
*
29830 CAGAGGCA
1 CGGAGGCA
29838 ACAAGAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
CGGAGGCAGCAACGAGGGAAA
Found at i:30184 original size:43 final size:43
Alignment explanation
Indices: 30122--30306 Score: 226
Period size: 43 Copynumber: 4.3 Consensus size: 43
30112 ATCTGTGAAT
* * * **
30122 TTTAGTGGTGTTTGTGGAGAAAGCGCCACTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * *
30165 TTTAGCGGCGTTTATGGAGAAAGCGTCGCTAAAGGCCATGATC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
*
30208 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTGAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * **
30251 TTCAGCGGCATTTGTGGGGAAAGCGTTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
*
30294 TTTAACGGCGTTT
1 TTTAGCGGCGTTT
30307 TTCCTAATAA
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
Found at i:30470 original size:18 final size:18
Alignment explanation
Indices: 30447--30482 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30437 TAGTAAACAT
30447 AATCAATTCTTTTATCCA
1 AATCAATTCTTTTATCCA
30465 AATCAATTCTTTTATCCA
1 AATCAATTCTTTTATCCA
30483 TTCCGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
AATCAATTCTTTTATCCA
Found at i:30768 original size:39 final size:41
Alignment explanation
Indices: 30689--30778 Score: 148
Period size: 39 Copynumber: 2.2 Consensus size: 41
30679 TAAAAAGTAT
* *
30689 TTATATTAAAAAACACTATCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
30730 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
30769 TTATATTAAA
1 TTATATTAAA
30779 TATAATTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 30 0.64
40 1 0.02
41 16 0.34
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
Found at i:32485 original size:30 final size:30
Alignment explanation
Indices: 32423--32487 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
32413 TTTAACCTTT
* *
32423 CAAAA-TTTTTAAAAATTTTAATTAATCTC
1 CAAAACTTTTTAAAAATTTTAATTAAGCAC
* *
32452 CAAAACTTTTTAAATATTTTAATTAGGCAC
1 CAAAACTTTTTAAAAATTTTAATTAAGCAC
32482 CAAAAC
1 CAAAAC
32488 ATACATATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (30 bp):
CAAAACTTTTTAAAAATTTTAATTAAGCAC
Found at i:36914 original size:31 final size:30
Alignment explanation
Indices: 36852--36949 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 30
36842 AAATGCTCAC
* *
36852 ATAA-GGTCAAATC-TTTCAAATTGGTCAA
1 ATAAGGGTCAAATCTTTTCAAAGTGATCAA
36880 ATAAGGGTCAAATCTTTTCGAAAGTGATCAA
1 ATAAGGGTCAAATCTTTTC-AAAGTGATCAA
*** * * *
36911 ATAAATATCAAATATTTTTAAAAGTGCTCAA
1 ATAAGGGTCAAAT-CTTTTCAAAGTGATCAA
36942 ATAAGGGT
1 ATAAGGGT
36950 TTTCAAAATG
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
28 4 0.07
29 9 0.16
30 4 0.07
31 34 0.62
32 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (30 bp):
ATAAGGGTCAAATCTTTTCAAAGTGATCAA
Done.