Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008171.1 Kokia drynarioides strain JFW-HI SEQ_122830, 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: 97301
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:402 original size:2 final size:2
Alignment explanation
Indices: 395--420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
385 TTAATAGATG
395 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
421 GCGAAATTAA
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:5124 original size:68 final size:68
Alignment explanation
Indices: 5047--5182 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
5037 TTTATATCTA
*
5047 TATTTAAAAAAATAACCAAACTCCGTGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
1 TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
5112 ATT
66 ATT
*
5115 TATTTAAAAAAATAATCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
1 TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
5180 ATT
66 ATT
5183 CAAGTCGAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (68 bp):
TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
ATT
Found at i:13718 original size:17 final size:18
Alignment explanation
Indices: 13692--13733 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
13682 TGACAATGTC
13692 AAAA-AAAAAAAAAG-AA
1 AAAAGAAAAAAAAAGAAA
13708 AAAAGAAAAAAAAAGAAA
1 AAAAGAAAAAAAAAGAAA
13726 AAAAGAAA
1 AAAAGAAA
13734 TGTGCATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
18 10 0.42
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAA
Found at i:19062 original size:20 final size:20
Alignment explanation
Indices: 19026--19065 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19016 TTATGATATA
*
19026 AAAATAAATATTTTATATCT
1 AAAATAAATATTATATATCT
19046 AAAATAATATATATATATAT
1 AAAATAA-ATAT-TATATAT
19066 ATATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAAATATTATATATCT
Found at i:23046 original size:21 final size:22
Alignment explanation
Indices: 23016--23061 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
23006 ATAACAAAAA
*
23016 TAATTGTAATTATAACTAG-AAT
1 TAATTGTAA-TATAAATAGAAAT
23038 TAATT-TAATATAAATAGAAAT
1 TAATTGTAATATAAATAGAAAT
23059 TAA
1 TAA
23062 ACAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
TAATTGTAATATAAATAGAAAT
Found at i:31746 original size:18 final size:18
Alignment explanation
Indices: 31723--31760 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31713 TAGTATAGTT
31723 TTATTCG-GTTTATTAGAA
1 TTATTCGAG-TTATTAGAA
*
31741 TTATTCGAGTTATTTGAA
1 TTATTCGAGTTATTAGAA
31759 TT
1 TT
31761 TGAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATTCGAGTTATTAGAA
Found at i:31847 original size:23 final size:23
Alignment explanation
Indices: 31804--31848 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31794 AAAAAAATTC
**
31804 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
31827 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
31849 ATTCAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:36351 original size:4 final size:4
Alignment explanation
Indices: 36336--36374 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
36326 CTCCCTTCTC
*
36336 CCTT CTTT CCTT CCTT CCTT CCTT CCTT CCTT CC-T CCTT
1 CCTT CCTT CCTT CCTT CCTT CCTT CCTT CCTT CCTT CCTT
36375 TCTTGAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (4 bp):
CCTT
Found at i:44185 original size:11 final size:11
Alignment explanation
Indices: 44169--44195 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
44159 CATGGTAGAG
44169 GAAGATCAAGA
1 GAAGATCAAGA
44180 GAAGATCAAGA
1 GAAGATCAAGA
44191 GAAGA
1 GAAGA
44196 CACCTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.30, T:0.07
Consensus pattern (11 bp):
GAAGATCAAGA
Found at i:46869 original size:38 final size:39
Alignment explanation
Indices: 46819--46896 Score: 99
Period size: 38 Copynumber: 2.0 Consensus size: 39
46809 ATATAAAATT
46819 TTCAAAATTTTTTATAAAAAT-AGTAAAAAAA-TAAAAAA
1 TTCAAAATTTTTTATAAAAATCA-TAAAAAAAGTAAAAAA
* *
46857 TTCATAAA-TTTTTATAGAAATCATAAAAAAAGTATAAAA
1 TTCA-AAATTTTTTATAAAAATCATAAAAAAAGTAAAAAA
46896 T
1 T
46897 ACATCGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (39 bp):
TTCAAAATTTTTTATAAAAATCATAAAAAAAGTAAAAAA
Found at i:47190 original size:10 final size:10
Alignment explanation
Indices: 47177--47269 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
47167 TTTCTGTATA
47177 TTTTATAATT
1 TTTTATAATT
47187 TTTTA-AGA-T
1 TTTTATA-ATT
* **
47196 TATTATAAAA
1 TTTTATAATT
*
47206 TTTTACAATT
1 TTTTATAATT
47216 TTTTAT-ATT
1 TTTTATAATT
*
47225 TTTTGTACGA-T
1 TTTTATA--ATT
47236 TTTTAT-ATT
1 TTTTATAATT
*
47245 TTTT-CAATT
1 TTTTATAATT
*
47254 TTTAATAATT
1 TTTTATAATT
47264 TTTTAT
1 TTTTAT
47270 TAAAATTTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
8 1 0.02
9 26 0.43
10 27 0.44
11 6 0.10
12 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:47203 original size:19 final size:18
Alignment explanation
Indices: 47078--47268 Score: 77
Period size: 19 Copynumber: 10.0 Consensus size: 18
47068 TTCGTATGAT
47078 AATTTTTATAAATTTTTTTA
1 AATTTTTAT-AA-TTTTTTA
*
47098 ACGAATTTTAT-ATTTCTTTA
1 A--ATTTTTATAATTT-TTTA
* *
47118 TATTTTGTATAATTTTCTTTC
1 AATTTT-TATAA-TTT-TTTA
* **
47139 AA-CTTTATAAAATTTTA
1 AATTTTTATAATTTTTTA
*
47156 TAATTTTTAT-ATTTCTGTA
1 -AATTTTTATAATTT-TTTA
*
47175 TA-TTTTATAATTTTTTA
1 AATTTTTATAATTTTTTA
* **
47192 AGATTATTATAAAATTTTA
1 A-ATTTTTATAATTTTTTA
*
47211 CAATTTTTTATATTTTTTGTA
1 -AA-TTTTTATAATTTTT-TA
* *
47232 CGATTTTTAT-ATTTTTTC
1 -AATTTTTATAATTTTTTA
47250 AATTTTTAATAATTTTTTA
1 AATTTTT-ATAATTTTTTA
47269 TTAAAATTTG
Statistics
Matches: 126, Mismatches: 28, Indels: 35
0.67 0.15 0.19
Matches are distributed among these distances:
17 18 0.14
18 18 0.14
19 44 0.35
20 27 0.21
21 12 0.10
22 7 0.06
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTTTATAATTTTTTA
Found at i:47208 original size:55 final size:58
Alignment explanation
Indices: 47103--47225 Score: 157
Period size: 55 Copynumber: 2.2 Consensus size: 58
47093 TTTTAACGAA
* * *
47103 TTTTATATTTCTTTATATTTTGTATAATTTTCTTTCAACTTTATAAAATTTTATAA-T
1 TTTTATATTTCTGTATATTTTGTATAATTTTCTTTAAACTTTATAAAATTTTACAATT
*
47160 TTTTATATTTCTGTATA-TTT-TATAA-TTT-TTTAAGATTATTATAAAATTTTACAATT
1 TTTTATATTTCTGTATATTTTGTATAATTTTCTTTAA-ACT-TTATAAAATTTTACAATT
47216 TTTTATATTT
1 TTTTATATTT
47226 TTTGTACGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
53 4 0.07
54 5 0.08
55 20 0.34
56 14 0.24
57 16 0.27
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (58 bp):
TTTTATATTTCTGTATATTTTGTATAATTTTCTTTAAACTTTATAAAATTTTACAATT
Found at i:47431 original size:88 final size:88
Alignment explanation
Indices: 47331--47551 Score: 336
Period size: 88 Copynumber: 2.5 Consensus size: 88
47321 TTTAATAAAG
* * *
47331 GTAGGGGTTTAATTACTTTTTTTGAAAAAGTTGGAGGGTCTTTTTGATGCATTTTAAAAGTTCAA
1 GTAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTTGATGCATTTTAAAAGTTCAA
* *
47396 GTACCCAATTGAGTGC-AAAAAAA
65 ATACCCAAATGAGTGCAAAAAAAA
* *
47419 GTAGGGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAA
1 GTAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGC-TTTTTGATGCATTTTAAAAGTTCAA
47484 ATACCCAAATGAGTGCAAAAAAAA
65 ATACCCAAATGAGTGCAAAAAAAA
* *
47508 GGAGGGGCTTAATTGCTTTTTTTGAGAAAGTTTGAGGGCTTTTT
1 GTAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTT
47552 ACACCCTTAA
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
87 1 0.01
88 77 0.64
89 43 0.36
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (88 bp):
GTAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTGATGCATTTTAAAAGTTCAAA
TACCCAAATGAGTGCAAAAAAAA
Found at i:52234 original size:22 final size:22
Alignment explanation
Indices: 52209--52257 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
52199 TTTATGAAAA
*
52209 TTTTT-AAGAATTTTATGGTATT
1 TTTTTCAA-AATTTTAGGGTATT
*
52231 TTTTTCAAAATTTTAGGGTTTT
1 TTTTTCAAAATTTTAGGGTATT
52253 TTTTT
1 TTTTT
52258 GTTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTTCAAAATTTTAGGGTATT
Found at i:56664 original size:3 final size:3
Alignment explanation
Indices: 56656--56695 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
56646 ACATACAAAT
56656 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
56696 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:57535 original size:56 final size:56
Alignment explanation
Indices: 57449--57560 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
57439 ACAATACCAA
*
57449 AACGAATTACTTCATACTATGCGGGTTTCATTAGAAATAGTAGACATTATTATAAT
1 AACGAATTACTTCATACTATGCAGGTTTCATTAGAAATAGTAGACATTATTATAAT
* *
57505 AACGAATTACTTCATACTATGCAGGTTTCATTAGAAGTAGTAGACATTGTTATAAT
1 AACGAATTACTTCATACTATGCAGGTTTCATTAGAAATAGTAGACATTATTATAAT
57561 GATATAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (56 bp):
AACGAATTACTTCATACTATGCAGGTTTCATTAGAAATAGTAGACATTATTATAAT
Found at i:58950 original size:13 final size:13
Alignment explanation
Indices: 58932--58961 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
58922 TAAAAAAAAA
58932 TTTATTTTTTATT
1 TTTATTTTTTATT
58945 TTTATTTTTTATT
1 TTTATTTTTTATT
58958 TTTA
1 TTTA
58962 AACAAAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:58961 original size:6 final size:7
Alignment explanation
Indices: 58932--58960 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
58922 TAAAAAAAAA
58932 TTTATTT
1 TTTATTT
58939 TTTA-TT
1 TTTATTT
58945 TTTATTT
1 TTTATTT
58952 TTTATTT
1 TTTATTT
58959 TT
1 TT
58961 AAACAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:63502 original size:31 final size:31
Alignment explanation
Indices: 63464--63548 Score: 170
Period size: 31 Copynumber: 2.7 Consensus size: 31
63454 TAATCCATGT
63464 TAGTAGTATCTGCTTGTTTCAGCTGCAATGA
1 TAGTAGTATCTGCTTGTTTCAGCTGCAATGA
63495 TAGTAGTATCTGCTTGTTTCAGCTGCAATGA
1 TAGTAGTATCTGCTTGTTTCAGCTGCAATGA
63526 TAGTAGTATCTGCTTGTTTCAGC
1 TAGTAGTATCTGCTTGTTTCAGC
63549 CCCTAGATGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (31 bp):
TAGTAGTATCTGCTTGTTTCAGCTGCAATGA
Found at i:77045 original size:2 final size:2
Alignment explanation
Indices: 77038--77063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77028 TCAAATATTA
77038 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
77064 ATCAAAACAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:83656 original size:27 final size:27
Alignment explanation
Indices: 83626--83686 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
83616 ATATAAAAAA
*
83626 AAATTACTATTTTTAAAAAAATATTAG
1 AAATTAATATTTTTAAAAAAATATTAG
*
83653 AAATTTTAATATTTTTAAAAATATATTAG
1 AAA--TTAATATTTTTAAAAAAATATTAG
83682 AAATT
1 AAATT
83687 TTAATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
29 25 0.83
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (27 bp):
AAATTAATATTTTTAAAAAAATATTAG
Found at i:83693 original size:27 final size:29
Alignment explanation
Indices: 83633--83697 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
83623 AAAAAATTAC
83633 TATTTTTAAAAAAATATTAGAAATTTTAA
1 TATTTTTAAAAAAATATTAGAAATTTTAA
*
83662 TATTTTTAAAAATATATTAGAAATTTTAA
1 TATTTTTAAAAAAATATTAGAAATTTTAA
*
83691 TTTTTTT
1 TATTTTT
83698 TAAATTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TATTTTTAAAAAAATATTAGAAATTTTAA
Found at i:84489 original size:20 final size:19
Alignment explanation
Indices: 84461--84529 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
84451 TATAAAATTA
*
84461 TATAATTTTTATAATTTATT
1 TATATTTTTTATAATTT-TT
* *
84481 TATATTTTTTGTAAGTTTT
1 TATATTTTTTATAATTTTT
* *
84500 GATAATTTTTTTTATATTTTT
1 TAT-ATTTTTTATA-ATTTTT
84521 TAATATTTT
1 T-ATATTTT
84530 AAGAGGTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.10
20 23 0.59
21 10 0.26
22 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TATATTTTTTATAATTTTT
Found at i:92681 original size:2 final size:2
Alignment explanation
Indices: 92674--92704 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
92664 ACAAGTATGC
92674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
92705 AAGATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.