Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011281.1 Kokia drynarioides strain JFW-HI SEQ_126260, 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: 107899
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:2330 original size:60 final size:58
Alignment explanation
Indices: 2199--2333 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 58
2189 TTGATTTGTA
2199 TACCTAA-CTTTTTTTACCCAATTTGGTATTTGAACTTGATAATTTTTTCTAATTTGG
1 TACCTAAGCTTTTTTTACCCAATTTGGTATTTGAACTTGATAATTTTTTCTAATTTGG
* *
2256 TACCTAAGCCTTTTTTGGACCCAATTTGGTATTTGAACTTGGT-ATTTTTTCTTAATTTGG
1 TACCTAAG-CTTTTTT-TACCCAATTTGGTATTTGAACTTGATAATTTTTTC-TAATTTGG
* *
2316 TGCCTAAAGTTTTTTTTA
1 TACCT-AAGCTTTTTTTA
2334 ATATTCAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
57 7 0.10
59 16 0.24
60 42 0.62
61 3 0.04
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.50
Consensus pattern (58 bp):
TACCTAAGCTTTTTTTACCCAATTTGGTATTTGAACTTGATAATTTTTTCTAATTTGG
Found at i:2666 original size:89 final size:89
Alignment explanation
Indices: 2506--2673 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 89
2496 GATGATGTAG
* * *
2506 CAAATTAAGAAAAAGAGTCAAGTTTAAGTATTAAATTGGATCTCAAAAAGTTTAAGTATCAACTT
1 CAAATTAAGAAAAAGAATCAAGTTTAAGTATTAAATTGGATCTCAAAAAATTTAAGTATCAAATT
*
2571 ACAAAAATTGTCAAGTGTAGGTAT
66 ACAAAAAATGTCAAGTGTAGGTAT
* * *
2595 CAAATTAAGAAAAA-ATATTAAGTTTGAGTATTAAATTGGA-C-CAAAAAAATTTAGGTA-CTAA
1 CAAATTAAGAAAAAGA-ATCAAGTTTAAGTATTAAATTGGATCTC-AAAAAATTTAAGTATC-AA
*
2656 ATTAAGAAAAAATGTCAA
63 ATT-ACAAAAAATGTCAA
2674 ATTCAGGTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
87 2 0.03
88 18 0.27
89 47 0.70
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (89 bp):
CAAATTAAGAAAAAGAATCAAGTTTAAGTATTAAATTGGATCTCAAAAAATTTAAGTATCAAATT
ACAAAAAATGTCAAGTGTAGGTAT
Found at i:6216 original size:3 final size:3
Alignment explanation
Indices: 6208--6258 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
6198 GGAATCAAAC
6208 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6256 ATA
1 ATA
6259 GAAAAAGTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12433 original size:15 final size:15
Alignment explanation
Indices: 12413--12444 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12403 CATATTTTTT
*
12413 ATAATTTTAAAATAA
1 ATAATTTCAAAATAA
12428 ATAATTTCAAAATAA
1 ATAATTTCAAAATAA
12443 AT
1 AT
12445 TTTCATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTTCAAAATAA
Found at i:20627 original size:15 final size:15
Alignment explanation
Indices: 20607--20658 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
20597 CTCCGCTCTC
20607 TCTCTTTCTTCTATA
1 TCTCTTTCTTCTATA
20622 TCTC-TTCTATCTAT-
1 TCTCTTTCT-TCTATA
20636 TCT-TTTGCCTTCTATA
1 TCTCTTT--CTTCTATA
20652 TCTCTTT
1 TCTCTTT
20659 GCCTATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 9 0.29
15 14 0.45
16 5 0.16
17 3 0.10
ACGTcount: A:0.12, C:0.27, G:0.02, T:0.60
Consensus pattern (15 bp):
TCTCTTTCTTCTATA
Found at i:21919 original size:9 final size:9
Alignment explanation
Indices: 21901--21947 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
21891 TGAGGATGAG
*
21901 GATGACGAC
1 GATGAGGAC
21910 GATGAGGAC
1 GATGAGGAC
* *
21919 GAGGAGGAG
1 GATGAGGAC
*
21928 GATGACGAC
1 GATGAGGAC
21937 GATGAGGAC
1 GATGAGGAC
21946 GA
1 GA
21948 GGCAGTGGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.45, T:0.09
Consensus pattern (9 bp):
GATGAGGAC
Found at i:21958 original size:27 final size:27
Alignment explanation
Indices: 21886--21949 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
21876 GAGTGAAGAA
* *
21886 GAGGATGAGGATGAGGATGACGACGAT
1 GAGGACGAGGAGGAGGATGACGACGAT
21913 GAGGACGAGGAGGAGGATGACGACGAT
1 GAGGACGAGGAGGAGGATGACGACGAT
21940 GAGGACGAGG
1 GAGGACGAGG
21950 CAGTGGATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.48, T:0.09
Consensus pattern (27 bp):
GAGGACGAGGAGGAGGATGACGACGAT
Found at i:28843 original size:13 final size:13
Alignment explanation
Indices: 28825--28849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28815 TAGCCACTAC
28825 AAAAAATAAAAAT
1 AAAAAATAAAAAT
28838 AAAAAATAAAAA
1 AAAAAATAAAAA
28850 AAGGATTACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:30826 original size:25 final size:23
Alignment explanation
Indices: 30792--30838 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
30782 AATATAAAAA
*
30792 TATAAAATTATATTAGAAAGTAAAT
1 TATAAAATTAAATTA-AAA-TAAAT
*
30817 TATAATATTAAATTAAAATAAA
1 TATAAAATTAAATTAAAATAAA
30839 ATAACAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
TATAAAATTAAATTAAAATAAAT
Found at i:35626 original size:15 final size:16
Alignment explanation
Indices: 35598--35636 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
35588 GAGTTTCTTT
35598 TAAAAA-AT-ATAAAA
1 TAAAAATATAATAAAA
35612 T-AAAATATAATAAAA
1 TAAAAATATAATAAAA
35627 TAAAAATATA
1 TAAAAATATA
35637 TATTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
14 3 0.14
15 7 0.32
16 8 0.36
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATATAATAAAA
Found at i:35643 original size:21 final size:21
Alignment explanation
Indices: 35597--35645 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
35587 TGAGTTTCTT
35597 TTAA-AAAATATAAAATAAAA
1 TTAATAAAATATAAAATAAAA
*
35617 TATAATAAAATA-AAAATATATA
1 T-TAATAAAATATAAAATA-AAA
35639 TTAATAA
1 TTAATAA
35646 TTTCATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 15 0.60
22 9 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAATAAAATATAAAATAAAA
Found at i:35703 original size:20 final size:22
Alignment explanation
Indices: 35667--35708 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
35657 AAATATTTTT
35667 TATTTTATTAAGCAAA-TAAAA
1 TATTTTATTAAGCAAATTAAAA
35688 TATTTT-TTAA-CAAAATTAAAA
1 TATTTTATTAAGC-AAATTAAAA
35709 AATAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.05
20 7 0.37
21 11 0.58
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
TATTTTATTAAGCAAATTAAAA
Found at i:47129 original size:59 final size:59
Alignment explanation
Indices: 47037--47154 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
47027 TCCCACCAAA
** *
47037 AATGATTCGACTTTCGTCAGCATCACCACATGTTCTTTCATATCTTGTGCCCAACTTAC
1 AATGATTCGACTTTCGTCAGCATCACCACATGTTCCATCATATCTTATGCCCAACTTAC
47096 AATGATTCGACTTTCGTCAGCATCACCACATGTTCCATCATATCTTATGCCCAACTTAC
1 AATGATTCGACTTTCGTCAGCATCACCACATGTTCCATCATATCTTATGCCCAACTTAC
47155 TTAAATTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (59 bp):
AATGATTCGACTTTCGTCAGCATCACCACATGTTCCATCATATCTTATGCCCAACTTAC
Found at i:51648 original size:30 final size:31
Alignment explanation
Indices: 51612--51672 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
51602 TATGAGCACT
* * *
51612 ACTGTTACAT-CTTTTATCATTTTAGTCACC
1 ACTGTTACATAATTTAATCATATTAGTCACC
51642 ACTGTTACATAATTTAATCATATTAGTCACC
1 ACTGTTACATAATTTAATCATATTAGTCACC
51673 GGTCGTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.43
Consensus pattern (31 bp):
ACTGTTACATAATTTAATCATATTAGTCACC
Found at i:57022 original size:14 final size:15
Alignment explanation
Indices: 56993--57022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56983 TATTTTTAAA
56993 AACTTTAAATTATTT
1 AACTTTAAATTATTT
57008 AACTTTAAA-TATTT
1 AACTTTAAATTATTT
57022 A
1 A
57023 TTTTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
AACTTTAAATTATTT
Found at i:57388 original size:17 final size:18
Alignment explanation
Indices: 57363--57398 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
57353 TTTTAAAATA
*
57363 ATATTTGTTATTA-TTTT
1 ATATATGTTATTACTTTT
57380 ATATATGTTATTACTTTT
1 ATATATGTTATTACTTTT
57398 A
1 A
57399 AAAAATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
ATATATGTTATTACTTTT
Found at i:59342 original size:37 final size:37
Alignment explanation
Indices: 59293--59392 Score: 191
Period size: 37 Copynumber: 2.7 Consensus size: 37
59283 TCGGGTATAT
*
59293 AAAATTTATCATTTAATTTTTATGAATATCATAAATA
1 AAAATTTGTCATTTAATTTTTATGAATATCATAAATA
59330 AAAATTTGTCATTTAATTTTTATGAATATCATAAATA
1 AAAATTTGTCATTTAATTTTTATGAATATCATAAATA
59367 AAAATTTGTCATTTAATTTTTATGAA
1 AAAATTTGTCATTTAATTTTTATGAA
59393 ATTTATATTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (37 bp):
AAAATTTGTCATTTAATTTTTATGAATATCATAAATA
Found at i:72337 original size:39 final size:39
Alignment explanation
Indices: 72274--72401 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
72264 ACACATAAAG
* * *
72274 AGCAGAAGGCAATCATCCCCTACAATACGAGATACAAAA
1 AGCAGAATGCAATCGTCCCCTACAATATGAGATACAAAA
* **
72313 AGCAGAATGCAATCGTCCCTTACAATATGAGATACAAGG
1 AGCAGAATGCAATCGTCCCCTACAATATGAGATACAAAA
*
72352 AGCAGAATGCAATCGTCCCCTACAATATGAGATACAAAC
1 AGCAGAATGCAATCGTCCCCTACAATATGAGATACAAAA
72391 AGCAGAATGCA
1 AGCAGAATGCA
72402 CTTGTTCTCT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.16
Consensus pattern (39 bp):
AGCAGAATGCAATCGTCCCCTACAATATGAGATACAAAA
Found at i:76412 original size:129 final size:129
Alignment explanation
Indices: 76182--76437 Score: 415
Period size: 129 Copynumber: 2.0 Consensus size: 129
76172 GAACACCTGG
76182 TCATAACCATGCTGTCATTATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAACCAG
1 TCATAACCATGCTGTCATTATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAACCAG
* *
76247 ATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGCAAAG-TCCTGGATCGATAACTGTAA
66 ATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAG-AAAGATCCAGGATCAATAACTGTAA
* * ** *
76311 TCATAACCATGCTGTCATTATTGATCAACAGGCCCTGCCCTTACTGCAGCCAATTGAACAATCAG
1 TCATAACCATGCTGTCATTATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAACCAG
* *
76376 ATAGGAACTGTCAGTCTGAAGCAAACCAGCAATTACAAGAAAGATCCAGGGTCAATAACTGT
66 ATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGAAAGATCCAGGATCAATAACTGT
76438 GACCCTATAA
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 4 0.03
129 113 0.97
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (129 bp):
TCATAACCATGCTGTCATTATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAACCAG
ATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGAAAGATCCAGGATCAATAACTGTAA
Found at i:78224 original size:18 final size:18
Alignment explanation
Indices: 78186--78229 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
78176 GCACAAGAAC
*
78186 TTTTAATTATTTTATAATA
1 TTTT-ATTATTTTAGAATA
*
78205 TTTTATTATTTTAGATTA
1 TTTTATTATTTTAGAATA
78223 -TTTATTA
1 TTTTATTA
78230 AGTATTAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTATTATTTTAGAATA
Found at i:84227 original size:65 final size:65
Alignment explanation
Indices: 84146--84275 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
84136 GTTAATATGG
84146 GAATGTCACCTTAAAATGACAGTTGAGACGGATTGGCAAACAACTAAGGATCTAGGAATCTGCGT
1 GAATGTCACCTTAAAATGACAGTTGAGACGGATTGGCAAACAACTAAGGATCTAGGAATCTGCGT
84211 GAATGTCACCTTAAAATGACAGTTGAGACGGATTGGCAAACAACTAAGGATCTAGGAATCTGCGT
1 GAATGTCACCTTAAAATGACAGTTGAGACGGATTGGCAAACAACTAAGGATCTAGGAATCTGCGT
84276 ATCAAAATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (65 bp):
GAATGTCACCTTAAAATGACAGTTGAGACGGATTGGCAAACAACTAAGGATCTAGGAATCTGCGT
Found at i:103072 original size:56 final size:57
Alignment explanation
Indices: 102970--103078 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
102960 TCAAAAAGAT
** * *
102970 TATTTTTTTTATTTGTGTTTTTTGATGCCGATCATTAACTGTCAAACACCTAAAAAA
1 TATTTTTTTTATTCATGTTTTTTGATGCAGATCATTAACTGACAAACACCTAAAAAA
* * **
103027 TATTTTTTTTATTCATGTTTTTTGGTGCAGGT-ATTAGGTGACAAACACCTAA
1 TATTTTTTTTATTCATGTTTTTTGATGCAGATCATTAACTGACAAACACCTAA
103079 TTTTTTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
56 17 0.39
57 27 0.61
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.46
Consensus pattern (57 bp):
TATTTTTTTTATTCATGTTTTTTGATGCAGATCATTAACTGACAAACACCTAAAAAA
Done.