Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014901.1 Kokia drynarioides strain JFW-HI SEQ_129944, 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: 101697
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 313 characters in sequence are not A, C, G, or T
Found at i:7928 original size:24 final size:24
Alignment explanation
Indices: 7899--7947 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
7889 AAAGTGTTCC
7899 TTTTTTCAGACACTCTCTTGAAAA
1 TTTTTTCAGACACTCTCTTGAAAA
7923 TTTTTTCAGACACTCTCTTGAAAA
1 TTTTTTCAGACACTCTCTTGAAAA
7947 T
1 T
7948 CATTCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (24 bp):
TTTTTTCAGACACTCTCTTGAAAA
Found at i:22348 original size:21 final size:22
Alignment explanation
Indices: 22313--22353 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22303 TAATTAAGAG
*
22313 TTTAGGGTTTGGAATTTTAGTA
1 TTTAGGGATTGGAATTTTAGTA
22335 TTTAGGGATT-GAATTTTAG
1 TTTAGGGATTGGAATTTTAG
22354 AGCTCAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (22 bp):
TTTAGGGATTGGAATTTTAGTA
Found at i:31664 original size:20 final size:20
Alignment explanation
Indices: 31639--31681 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31629 ACATGATCGA
31639 CTTGCTATGATTATCAACTT
1 CTTGCTATGATTATCAACTT
* * *
31659 CTTGCTTTGCTTATTAACTT
1 CTTGCTATGATTATCAACTT
31679 CTT
1 CTT
31682 TTATTTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (20 bp):
CTTGCTATGATTATCAACTT
Found at i:34283 original size:78 final size:78
Alignment explanation
Indices: 34188--34336 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 78
34178 TAATCTCCTA
* ** * *
34188 AAAATGATAAAATTTTATTTAATCCTTT-AAAATT-TTTTTTTATTATCATAAAAATTACAATTT
1 AAAATGATAAAAATTTATTTAATCCTTTAAAAATTACATTTTTACTATAAT-AAAATTACAATTT
34251 AACTTCGTTCCCCT
65 AACTTCGTTCCCCT
*
34265 AAAATGATAAAAAATTTATTTAATTCTTTAAAAATTACATTTTTACTATAATAAAATTACAATTT
1 AAAATGAT-AAAAATTTATTTAATCCTTTAAAAATTACATTTTTACTATAATAAAATTACAATTT
34330 AACTTCG
65 AACTTCG
34337 ACCTTAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
77 8 0.13
78 18 0.29
79 26 0.41
80 11 0.17
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (78 bp):
AAAATGATAAAAATTTATTTAATCCTTTAAAAATTACATTTTTACTATAATAAAATTACAATTTA
ACTTCGTTCCCCT
Found at i:54147 original size:30 final size:30
Alignment explanation
Indices: 54111--54171 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
54101 GTTCTTCCCT
54111 TGTGATGATCTCTCTTTTTCTCTAATTTCA
1 TGTGATGATCTCTCTTTTTCTCTAATTTCA
54141 TGTGATGATCTCTCTTTTTCTCTAATTTCA
1 TGTGATGATCTCTCTTTTTCTCTAATTTCA
54171 T
1 T
54172 ACTGTATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (30 bp):
TGTGATGATCTCTCTTTTTCTCTAATTTCA
Found at i:60557 original size:52 final size:51
Alignment explanation
Indices: 60465--60564 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 51
60455 TTAGAAATGA
*
60465 TAAGAAAATATTAATTAATTATTTAATTTTATTCCATTAATTATTATGATTT
1 TAAGAAAATATTAATTAATTATTTAATTTTAAT-CATTAATTATTATGATTT
60517 TAAGAAAATATT-ATTAAATTATTTAATTTTAAAT-AGTTAATTATTATG
1 TAAGAAAATATTAATT-AATTATTTAATTTT-AATCA-TTAATTATTATG
60565 TTGTTCATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
51 4 0.09
52 38 0.86
53 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (51 bp):
TAAGAAAATATTAATTAATTATTTAATTTTAATCATTAATTATTATGATTT
Found at i:62897 original size:25 final size:24
Alignment explanation
Indices: 62868--62941 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 24
62858 AAAATACATA
62868 TATTTATTTTTCATATATGTTATTC
1 TATTTATTTTTCATATAT-TTATTC
**
62893 TATTT-TCTTTTCCCATATTTGATTC
1 TATTTAT-TTTTCATATATTT-ATTC
*
62918 --TTTATTTTTCATATAAATTATTC
1 TATTTATTTTTCATAT-ATTTATTC
62941 T
1 T
62942 TTTTCCTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
23 14 0.36
24 7 0.18
25 18 0.46
ACGTcount: A:0.23, C:0.12, G:0.03, T:0.62
Consensus pattern (24 bp):
TATTTATTTTTCATATATTTATTC
Found at i:62940 original size:23 final size:23
Alignment explanation
Indices: 62870--62943 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
62860 AATACATATA
**
62870 TTTATTTTTCATATATGTTATTC
1 TTTATTTTTCATATAAATTATTC
* ** *
62893 TATTTTCTTTTCCCAT-ATTTGATTC
1 T-TTAT-TTTTCATATAAATT-ATTC
62918 TTTATTTTTCATATAAATTATTC
1 TTTATTTTTCATATAAATTATTC
62941 TTT
1 TTT
62944 TTCCTCTCCT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
23 15 0.39
24 11 0.29
25 12 0.32
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.64
Consensus pattern (23 bp):
TTTATTTTTCATATAAATTATTC
Found at i:62964 original size:47 final size:48
Alignment explanation
Indices: 62870--62979 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 48
62860 AATACATATA
** * *
62870 TTTATTTTTCATATATGTTATTCTATTTTCTTTTCCCATATTTGATTC
1 TTTATTTTTCATATAAATTATTCTATTTTCCTCTCCCATATTTGATTC
*
62918 TTTATTTTTCATATAAATTATTCT-TTTTCCTCTCCTATATTTGATTC
1 TTTATTTTTCATATAAATTATTCTATTTTCCTCTCCCATATTTGATTC
*
62965 CTTA-TTTTC-TATAAA
1 TTTATTTTTCATATAAA
62980 AAATTTAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 6 0.11
46 5 0.09
47 23 0.41
48 22 0.39
ACGTcount: A:0.22, C:0.15, G:0.03, T:0.60
Consensus pattern (48 bp):
TTTATTTTTCATATAAATTATTCTATTTTCCTCTCCCATATTTGATTC
Found at i:63077 original size:19 final size:18
Alignment explanation
Indices: 63053--63113 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
63043 TGATTTTTTC
*
63053 TCTCTCGTCCTTTTATCTT
1 TCTCTCGT-CTTCTATCTT
* * * *
63072 TCTCTCAT-ATGTATTTT
1 TCTCTCGTCTTCTATCTT
63089 TCTCTCGTTCTTCTATCTT
1 TCTCTCG-TCTTCTATCTT
63108 TCTCTC
1 TCTCTC
63114 ATATCTCTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 12 0.38
18 1 0.03
19 19 0.59
ACGTcount: A:0.08, C:0.30, G:0.05, T:0.57
Consensus pattern (18 bp):
TCTCTCGTCTTCTATCTT
Found at i:63106 original size:36 final size:37
Alignment explanation
Indices: 63048--63117 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
63038 ATATTTGATT
*
63048 TTTTCTCTCTCGTCCTTTTATCTTTCTCTCATATGTA
1 TTTTCTCTCTCGTCCTTCTATCTTTCTCTCATATGTA
*
63085 TTTT-TCTCTCGTTCTTCTATCTTTCTCTCATAT
1 TTTTCTCTCTCGTCCTTCTATCTTTCTCTCATAT
63118 CTCTTTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.10, C:0.27, G:0.04, T:0.59
Consensus pattern (37 bp):
TTTTCTCTCTCGTCCTTCTATCTTTCTCTCATATGTA
Found at i:63126 original size:19 final size:19
Alignment explanation
Indices: 63068--63127 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
63058 CGTCCTTTTA
* *
63068 TCTTTCTCTCATATGT-AT
1 TCTTTCTCTCATATCTCTT
* *
63086 T-TTTCTCTCGT-TCTTCTA
1 TCTTTCTCTCATATC-TCTT
63104 TCTTTCTCTCATATCTCTT
1 TCTTTCTCTCATATCTCTT
63123 TCTTT
1 TCTTT
63128 TTCACTCTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
16 1 0.03
17 10 0.31
18 2 0.06
19 17 0.53
20 2 0.06
ACGTcount: A:0.10, C:0.27, G:0.03, T:0.60
Consensus pattern (19 bp):
TCTTTCTCTCATATCTCTT
Found at i:65092 original size:91 final size:89
Alignment explanation
Indices: 64997--65202 Score: 245
Period size: 91 Copynumber: 2.3 Consensus size: 89
64987 AACTCTTTGC
* * * * *
64997 TTTTATTTTGCACTCATTTGAATACTTGAACTTTCAAAATGCATCAAAAA-AGTCCTCAAATTTA
1 TTTTATTTTGCACTCAATTGGATACTTGAACTTTCAAAATACATCAAAAAGA-CCCTCAAACTTA
* *
65061 AAAAAAAAAATGAAATTAAGCCCTTGT
65 AAAAAAAAAA--AAATTAAGCCCCTGA
* * * * * *
65088 TTTTATTTTCCAATCAATTGGATACTTGAACTTTTAAAATATATCTAAAAGACCCTCAGACTTAA
1 TTTTATTTTGCACTCAATTGGATACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAACTTAA
*
65153 AAAAAAAAACAATTAAGCCCCTGA
66 AAAAAAAAAAAATTAAGCCCCTGA
65177 TTTT-TTTTGCACTCAATTGGATACTT
1 TTTTATTTTGCACTCAATTGGATACTT
65203 TAACCGCCCC
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
88 20 0.20
89 16 0.16
91 61 0.62
92 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (89 bp):
TTTTATTTTGCACTCAATTGGATACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAACTTAA
AAAAAAAAAAAATTAAGCCCCTGA
Found at i:65323 original size:19 final size:17
Alignment explanation
Indices: 65299--65368 Score: 54
Period size: 19 Copynumber: 3.9 Consensus size: 17
65289 TTTTTGATGC
65299 ATTTTATATATATTTTTTA
1 ATTTT-TAT-TATTTTTTA
* *
65318 ATTTTAAATTTTTTTTCTA
1 ATTTT-TATTATTTTT-TA
65337 ATTTTTATTGA-TTTTT-
1 ATTTTTATT-ATTTTTTA
*
65353 ATTTTTATAATTTTTT
1 ATTTTTATTATTTTTT
65369 TTTTGCGACA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.02
16 13 0.30
17 1 0.02
18 13 0.30
19 15 0.35
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (17 bp):
ATTTTTATTATTTTTTA
Found at i:72330 original size:20 final size:19
Alignment explanation
Indices: 72305--72343 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
72295 ACTTACAATT
72305 TTTCTCATATTTTTCATATA
1 TTTCTCAT-TTTTTCATATA
*
72325 TTTCTCATTTTTTTATATA
1 TTTCTCATTTTTTCATATA
72344 ATTGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTCTCATTTTTTCATATA
Found at i:73708 original size:2 final size:2
Alignment explanation
Indices: 73701--73729 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73691 ATTAAATGTG
73701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73730 TCAAAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79418 original size:19 final size:21
Alignment explanation
Indices: 79381--79419 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
79371 TGTCTAATAG
*
79381 AAAAGCAAAATAAATAGAAAA
1 AAAAGCAAAAGAAATAGAAAA
79402 AAAAG-AAAAGAAA-AGAAA
1 AAAAGCAAAAGAAATAGAAA
79420 GTAACCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (21 bp):
AAAAGCAAAAGAAATAGAAAA
Found at i:81721 original size:43 final size:43
Alignment explanation
Indices: 81660--81747 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
81650 AAGAGGTCTT
81660 CCATTCCAACATAACCAAATACTCGGTAAAATAATCTAACCAA
1 CCATTCCAACATAACCAAATACTCGGTAAAATAATCTAACCAA
81703 CCATTCCAACATAACCAAATACTCGGTAAAATAATCTAACCAA
1 CCATTCCAACATAACCAAATACTCGGTAAAATAATCTAACCAA
81746 CC
1 CC
81748 CCCAAAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (43 bp):
CCATTCCAACATAACCAAATACTCGGTAAAATAATCTAACCAA
Found at i:84514 original size:56 final size:56
Alignment explanation
Indices: 84447--84559 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
84437 AGCTTCTTGC
*
84447 CAGTTAGTACTTTTGCTTAATCAATCATTTATTAATTAAAAAGAAAAAGGAGTTGT
1 CAGTTAGTACTTTTGCTTAATCAATCATTTATTAATTAAAAAGAAAAAGGAATTGT
*
84503 CAGTTAGTACTTTTGCTTAATCAATCATTTATTAATTAAAAAGAAAAATGAATTGT
1 CAGTTAGTACTTTTGCTTAATCAATCATTTATTAATTAAAAAGAAAAAGGAATTGT
84559 C
1 C
84560 CATTGGTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (56 bp):
CAGTTAGTACTTTTGCTTAATCAATCATTTATTAATTAAAAAGAAAAAGGAATTGT
Found at i:94391 original size:43 final size:43
Alignment explanation
Indices: 94309--94393 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
94299 ATTAACATGT
* **
94309 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCATGCATGTTAC
* *
94352 TAAATTATATTACTTTACTCTTATTAATAT-CATGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCATG-CATGTTA
94394 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCATGCATGTTAC
Found at i:95061 original size:45 final size:45
Alignment explanation
Indices: 94945--95081 Score: 141
Period size: 45 Copynumber: 3.0 Consensus size: 45
94935 GCATAGCTCA
* * * *
94945 TCAAGCCAAGGATATCAGCCTCAA-TTTGAGGAGCCACCGCAACAC
1 TCAAGCCAAGGATATCAACCT-AAGTTTAACGAGCCACCGCAATAC
*
94990 TCAAGCCAATGATATCAACCTAAGTTTAACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAACCTAAGTTTAACGAGCCACCGCAATAC
** ** * * * *
95035 TCAAGGGAAGGATATCAAGTTGAGTTTGATGAGCCACCGTAATAC
1 TCAAGCCAAGGATATCAACCTAAGTTTAACGAGCCACCGCAATAC
95080 TC
1 TC
95082 TACTCCTTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 2 0.03
45 75 0.97
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAACCTAAGTTTAACGAGCCACCGCAATAC
Found at i:96473 original size:4 final size:4
Alignment explanation
Indices: 96453--96501 Score: 73
Period size: 4 Copynumber: 12.2 Consensus size: 4
96443 AACACATTAC
*
96453 CTTT CTTT CATT C-TT CTTT CTTT CTTT CTTT CTTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT
96501 C
1 C
96502 CCGTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
3 3 0.07
4 35 0.83
5 4 0.10
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:98366 original size:14 final size:12
Alignment explanation
Indices: 98334--98360 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
98324 GGGTAGTTAG
98334 GAGGTTAGCAGA
1 GAGGTTAGCAGA
98346 GAGGTTAGCAGA
1 GAGGTTAGCAGA
98358 GAG
1 GAG
98361 CAGTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.44, T:0.15
Consensus pattern (12 bp):
GAGGTTAGCAGA
Done.