Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009736.1 Kokia drynarioides strain JFW-HI SEQ_124455, 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: 142179
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6292 original size:17 final size:17
Alignment explanation
Indices: 6270--6313 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
6260 TACGATTTTA
*
6270 TTTATTTATTATTTATT
1 TTTATTTAGTATTTATT
* *
6287 TTTATTAAGTATTTGTT
1 TTTATTTAGTATTTATT
6304 TTTATTTAGT
1 TTTATTTAGT
6314 TTCAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTATTTAGTATTTATT
Found at i:20647 original size:17 final size:16
Alignment explanation
Indices: 20613--20671 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
20603 AGTATAAAAT
20613 ATTAAAAATTTAAAATAA
1 ATTAAAAA-TT-AAATAA
20631 ATTAATAAATTAAATAA
1 ATTAA-AAATTAAATAA
*
20648 ATTAAAAATTAGA-AA
1 ATTAAAAATTAAATAA
20663 A-TAAAAATT
1 ATTAAAAATT
20672 TCTTACCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
14 8 0.21
15 3 0.08
16 7 0.18
17 11 0.28
18 7 0.18
19 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATTAAAAATTAAATAA
Found at i:20648 original size:9 final size:9
Alignment explanation
Indices: 20625--20653 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
20615 TAAAAATTTA
20625 AAATAAATT
1 AAATAAATT
20634 -AATAAATT
1 AAATAAATT
20642 AAATAAATT
1 AAATAAATT
20651 AAA
1 AAA
20654 AATTAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAATAAATT
Found at i:23739 original size:24 final size:25
Alignment explanation
Indices: 23712--23759 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
23702 TGTAAAAACT
*
23712 AAAGA-AACAAATTAA-AGTAAAATA
1 AAAGACAA-AAATTAATAGAAAAATA
23736 AAAGACAAAAATTAATAGAAAAAT
1 AAAGACAAAAATTAATAGAAAAAT
23760 TACAATGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (25 bp):
AAAGACAAAAATTAATAGAAAAATA
Found at i:31145 original size:29 final size:29
Alignment explanation
Indices: 31103--31160 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
31093 TCAGTGGTAG
31103 TACAATAGTAAAATTGTATTGACAATAAA
1 TACAATAGTAAAATTGTATTGACAATAAA
31132 TACAATAGTAAAATTGTATTGACAATAAA
1 TACAATAGTAAAATTGTATTGACAATAAA
31161 GTCCAAGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (29 bp):
TACAATAGTAAAATTGTATTGACAATAAA
Found at i:49415 original size:15 final size:15
Alignment explanation
Indices: 49395--49430 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49385 GACAGTGTTT
49395 TCAGCAGATTCTTTC
1 TCAGCAGATTCTTTC
**
49410 TCAGCATCTTCTTTC
1 TCAGCAGATTCTTTC
49425 TCAGCA
1 TCAGCA
49431 TTTTCTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.31, G:0.11, T:0.39
Consensus pattern (15 bp):
TCAGCAGATTCTTTC
Found at i:49431 original size:15 final size:15
Alignment explanation
Indices: 49403--49437 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
49393 TTTCAGCAGA
49403 TTCTTTCTCAGCATC
1 TTCTTTCTCAGCATC
*
49418 TTCTTTCTCAGCATT
1 TTCTTTCTCAGCATC
49433 TTCTT
1 TTCTT
49438 CCTCGTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.29, G:0.06, T:0.54
Consensus pattern (15 bp):
TTCTTTCTCAGCATC
Found at i:60569 original size:3 final size:3
Alignment explanation
Indices: 60511--60552 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
60501 TACAGATTTA
60511 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
60553 TTCATTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:68649 original size:16 final size:16
Alignment explanation
Indices: 68628--68661 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
68618 AAAATTGATA
68628 AAACTAACAAGAAATT
1 AAACTAACAAGAAATT
* *
68644 AAACTAACTAGTAATT
1 AAACTAACAAGAAATT
68660 AA
1 AA
68662 TTAGAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
AAACTAACAAGAAATT
Found at i:72157 original size:12 final size:12
Alignment explanation
Indices: 72142--72166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72132 ATTAAATAAT
72142 TAATAGCATTCA
1 TAATAGCATTCA
72154 TAATAGCATTCA
1 TAATAGCATTCA
72166 T
1 T
72167 CATAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:75618 original size:21 final size:21
Alignment explanation
Indices: 75570--75646 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
75560 CATAGTGCAG
*
75570 ACTTCTACCGATACAAGTGAG
1 ACTTCTACCGATACAAGTGAC
** *
75591 AGGTCTACTGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * *
75612 TCTTCTACCGAAACAAGT-ATT
1 ACTTCTACCGATACAAGTGA-C
*
75633 ACTTCTACCCATAC
1 ACTTCTACCGATAC
75647 TAAAAACTCT
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:81344 original size:15 final size:16
Alignment explanation
Indices: 81306--81351 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
81296 TTTGGAAATA
81306 ACCCTATGAAATCTAT
1 ACCCTATGAAATCTAT
81322 ACCCTATGAAATCTAT
1 ACCCTATGAAATCTAT
81338 A-CCTATGAAATCTA
1 ACCCTATGAAATCTA
81352 GCACAACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (16 bp):
ACCCTATGAAATCTAT
Found at i:87343 original size:52 final size:52
Alignment explanation
Indices: 87207--87387 Score: 213
Period size: 52 Copynumber: 3.5 Consensus size: 52
87197 TCAATATTTA
** * * ** * *
87207 ATACTCACGATGACACAAAGTCATCGGACCT-TTAATTCATTAAA-GAATCAC
1 ATACTCACGATGACACGTAGTCATCGAACCTCATAA-TCCGTAAAGGATTCAT
* * *
87258 ATACTCACGATGACACATAGACATCAAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* *
87310 ATACTCACGATGACATGTAGTCATCGAATCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
*
87362 ATACTCACGATAACACGTAGTCATCG
1 ATACTCACGATGACACGTAGTCATCG
87388 GACTTTTTTC
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
51 33 0.29
52 79 0.71
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:100263 original size:6 final size:6
Alignment explanation
Indices: 100252--100277 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
100242 GTGAGCGCCC
100252 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
100278 CAAAGGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:100984 original size:13 final size:12
Alignment explanation
Indices: 100960--101004 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
100950 CAATCACTTG
*
100960 AAAAAAATGAGA
1 AAAAAAAAGAGA
100972 AAAAAGAAAGAGA
1 AAAAA-AAAGAGA
*
100985 AAAGAAAAGAAGA
1 AAAAAAAAG-AGA
100998 AAAAAAA
1 AAAAAAA
101005 TTATTGGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:106400 original size:52 final size:52
Alignment explanation
Indices: 106336--106522 Score: 293
Period size: 52 Copynumber: 3.6 Consensus size: 52
106326 AAAGAATCGC
* *
106336 ATACTCAGGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * **
106388 ATACTCATGATGACACGTCGTCATTGGACCTCATAATCTATAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
106440 ATACTCACGATGACACGTAGTTATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
106492 ATACTCACGATGACACGTAGTCATTGGACCT
1 ATACTCACGATGACACGTAGTCATCGGACCT
106523 TCTTCATTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:108153 original size:28 final size:28
Alignment explanation
Indices: 108122--108273 Score: 130
Period size: 28 Copynumber: 5.4 Consensus size: 28
108112 TTTCCATGCC
* *
108122 AGAATCAAAATATCACTCTTTTCGAGTT
1 AGAATCAGAATATCACTCTTTTCGAGCT
* * *
108150 AGAATTAGAATATTAATCTTTTCGAGCCT
1 AGAATCAGAATATCACTCTTTTCGAG-CT
* ** *
108179 -GAATCAGAATATCGCTCTTCCCGAGCA
1 AGAATCAGAATATCACTCTTTTCGAGCT
*
108206 AGAATCAGAATATCGCTCTTTTCGAGCT
1 AGAATCAGAATATCACTCTTTTCGAGCT
** *
108234 AGAAAT-AGAATAAT-ACTCTACTCGAGCC
1 AG-AATCAGAAT-ATCACTCTTTTCGAGCT
*
108262 AGAAACAGAATA
1 AGAATCAGAATA
108274 ACGCTTTACC
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
27 4 0.04
28 89 0.90
29 6 0.06
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (28 bp):
AGAATCAGAATATCACTCTTTTCGAGCT
Found at i:108274 original size:28 final size:28
Alignment explanation
Indices: 108171--108358 Score: 110
Period size: 28 Copynumber: 6.7 Consensus size: 28
108161 ATTAATCTTT
* * * * *
108171 TCGAGCCTGAATCAGAATATCGCTCTTC
1 TCGAGCCAGAAACAGAATAACACTCTAC
* * * * * **
108199 CCGAGCAAGAATCAGAATATCGCTCTTT
1 TCGAGCCAGAAACAGAATAACACTCTAC
* * *
108227 TCGAGCTAGAAATAGAATAATACTCTAC
1 TCGAGCCAGAAACAGAATAACACTCTAC
* *
108255 TCGAGCCAGAAACAGAATAACGCTTTAC
1 TCGAGCCAGAAACAGAATAACACTCTAC
* * * *
108283 CCGAGCAAGAAACAAAATAACGCTCTAC
1 TCGAGCCAGAAACAGAATAACACTCTAC
* * * *
108311 -CTGAGCCAAAAACAAAATATCACTTTA-
1 TC-GAGCCAGAAACAGAATAACACTCTAC
*
108338 TCCGAGCCAAAAACAGAATAA
1 T-CGAGCCAGAAACAGAATAA
108359 AACTAGCGAG
Statistics
Matches: 128, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
27 1 0.01
28 126 0.98
29 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.20
Consensus pattern (28 bp):
TCGAGCCAGAAACAGAATAACACTCTAC
Found at i:108288 original size:56 final size:56
Alignment explanation
Indices: 108228--108358 Score: 140
Period size: 56 Copynumber: 2.3 Consensus size: 56
108218 TCGCTCTTTT
* * * * * *
108228 CGAGCTAGAAATAGAATAATACTCTA-CTCGAGCCAGAAACAGAATAACGCTTTACC
1 CGAGCAAGAAACAGAATAACACTCTACCT-GAGCCAAAAACAAAATAACACTTTACC
* * * *
108284 CGAGCAAGAAACAAAATAACGCTCTACCTGAGCCAAAAACAAAATATCACTTTATC
1 CGAGCAAGAAACAGAATAACACTCTACCTGAGCCAAAAACAAAATAACACTTTACC
108340 CGAGCCAA-AAACAGAATAA
1 CGAG-CAAGAAACAGAATAA
108359 AACTAGCGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
56 57 0.92
57 5 0.08
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.17
Consensus pattern (56 bp):
CGAGCAAGAAACAGAATAACACTCTACCTGAGCCAAAAACAAAATAACACTTTACC
Found at i:108307 original size:84 final size:84
Alignment explanation
Indices: 108122--108308 Score: 241
Period size: 84 Copynumber: 2.2 Consensus size: 84
108112 TTTCCATGCC
* * * * ** * *
108122 AGAATCAAAATATCACTCTTTTCGAGTTAGAATTAGAATATTAATCTTTTCGAGCCTGAATCAGA
1 AGAATCAAAATATCGCTCTTTTCGAGCTAGAAATAGAATAATAATCTACTCGAGCCAGAAACAGA
*
108187 ATATCGCTCTTCCCGAGCA
66 ATAACGCTCTTCCCGAGCA
* *
108206 AGAATCAGAATATCGCTCTTTTCGAGCTAGAAATAGAATAATACTCTACTCGAGCCAGAAACAGA
1 AGAATCAAAATATCGCTCTTTTCGAGCTAGAAATAGAATAATAATCTACTCGAGCCAGAAACAGA
108271 ATAACGCT-TTACCCGAGCA
66 ATAACGCTCTT-CCCGAGCA
* *
108290 AGAAACAAAATAACGCTCT
1 AGAATCAAAATATCGCTCT
108309 ACCTGAGCCA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 2 0.02
84 86 0.98
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (84 bp):
AGAATCAAAATATCGCTCTTTTCGAGCTAGAAATAGAATAATAATCTACTCGAGCCAGAAACAGA
ATAACGCTCTTCCCGAGCA
Found at i:119080 original size:33 final size:33
Alignment explanation
Indices: 119038--119103 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
119028 AATGAGATAA
119038 TCGAGTAGCTATTATTTCGCTACACGAAGGTTT
1 TCGAGTAGCTATTATTTCGCTACACGAAGGTTT
119071 TCGAGTAGCTATTATTTCGCTACACGAAGGTTT
1 TCGAGTAGCTATTATTTCGCTACACGAAGGTTT
119104 ATGAATTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (33 bp):
TCGAGTAGCTATTATTTCGCTACACGAAGGTTT
Found at i:122335 original size:3 final size:3
Alignment explanation
Indices: 122327--122352 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
122317 TTCTTTAGTT
122327 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
122353 TGGGTGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:139478 original size:28 final size:28
Alignment explanation
Indices: 139445--139499 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
139435 TAGTAACAGG
*
139445 TATGACTTTTGGGTCAACAAGGAGTAAC
1 TATGACCTTTGGGTCAACAAGGAGTAAC
*
139473 TATGACCTTTGGGTCAACAGGGAGTAA
1 TATGACCTTTGGGTCAACAAGGAGTAA
139500 TCAGATAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (28 bp):
TATGACCTTTGGGTCAACAAGGAGTAAC
Done.