Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011364.1 Kokia drynarioides strain JFW-HI SEQ_126345, 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: 36100
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:330 original size:97 final size:96
Alignment explanation
Indices: 219--399 Score: 281
Period size: 97 Copynumber: 1.9 Consensus size: 96
209 TAATTATGCT
* * *
219 TCATTAAGTGTTTTGTTCGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAGTGTTTTGTT
1 TCATTAAGTATTTTGTTCGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAATGTGTTGTT
284 TGTTGAAATGCATCTTTGTTTAATAATCTGCA
66 TGTT-AAATGCATCTTTGTTTAATAATCTGCA
* * * * *
316 TCATTAAGTATTTTGTTTGTTAAATGCATCTTTGTTTAGTAATTTTCATTATTAAATGTGTTGTT
1 TCATTAAGTATTTTGTTCGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAATGTGTTGTT
381 TGTTAAATGCATCTTTGTT
66 TGTTAAATGCATCTTTGTT
400 CAATGCCTTG
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
96 15 0.20
97 61 0.80
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.51
Consensus pattern (96 bp):
TCATTAAGTATTTTGTTCGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAATGTGTTGTT
TGTTAAATGCATCTTTGTTTAATAATCTGCA
Found at i:414 original size:48 final size:48
Alignment explanation
Indices: 219--399 Score: 281
Period size: 48 Copynumber: 3.8 Consensus size: 48
209 TAATTATGCT
*
219 TCATTAAGTGTTTTGTTCGTTAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
267 TCATTAAGTGTTTTGTTTGTTGAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTT-AAATGCATCTTTGTTTAATAATCTGCA
* * * *
316 TCATTAAGTATTTTGTTTGTTAAATGCATCTTTGTTTAGTAATTTTCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
* * *
364 TTATTAAATGTGTTGTTTGTTAAATGCATCTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
400 CAATGCCTTG
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
48 76 0.62
49 47 0.38
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.51
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
Found at i:4228 original size:97 final size:96
Alignment explanation
Indices: 4118--4298 Score: 290
Period size: 97 Copynumber: 1.9 Consensus size: 96
4108 TAATTTTGCT
*
4118 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATCATTAAGTATTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATCATTAAATATTTTGTT
*
4183 TGTTAAAATGCATCTTTGTTTAATAATATGCA
66 TATT-AAATGCATCTTTGTTTAATAATATGCA
* * * * *
4215 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTACTAATTTTCATTATTAAATGTTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATCATTAAATATTTTGTT
4280 TATTAAATGCATCTTTGTT
66 TATTAAATGCATCTTTGTT
4299 CAATGCCTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 15 0.19
97 62 0.81
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (96 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATCATTAAATATTTTGTT
TATTAAATGCATCTTTGTTTAATAATATGCA
Found at i:4313 original size:48 final size:48
Alignment explanation
Indices: 4118--4298 Score: 272
Period size: 48 Copynumber: 3.8 Consensus size: 48
4108 TAATTTTGCT
* *
4118 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCA
*
4166 TCATTAAGTATTTTGTTTGTTAAAATGCATCTTTGTTTAATAATATGCA
1 TCATTAAGTGTTTTGTTTGTT-AAATGCATCTTTGTTTAATAATATGCA
* * *
4215 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTACTAATTTTCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCA
* * *
4263 TTATTAAATGTTTTGTTTATTAAATGCATCTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
4299 CAATGCCTTG
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
48 77 0.63
49 45 0.37
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCA
Found at i:6361 original size:30 final size:31
Alignment explanation
Indices: 6292--6377 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 31
6282 AGCACTAGTT
* ** * *
6292 TTGCAATCACTCATGTTGCAAACACTAGAGA
1 TTGCAAACACTCATGTTGTGAACACTACACA
*
6323 -TGCGAACACTCATGTTGTGAACAC-ACACA
1 TTGCAAACACTCATGTTGTGAACACTACACA
* * *
6352 TTGCAAACACTGATATCGTGAACACT
1 TTGCAAACACTCATGTTGTGAACACT
6378 CGTATTACAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 3 0.07
30 40 0.93
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (31 bp):
TTGCAAACACTCATGTTGTGAACACTACACA
Found at i:9951 original size:19 final size:19
Alignment explanation
Indices: 9927--9978 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
9917 TAAAAGTTAG
9927 TATAAGTGGTTTGGTTTAA
1 TATAAGTGGTTTGGTTTAA
9946 TATAAGTGGTTTGGTTTAA
1 TATAAGTGGTTTGGTTTAA
*
9965 AAGTCAAGTGGTTT
1 TA-T-AAGTGGTTT
9979 TAAAAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 20 0.67
20 1 0.03
21 9 0.30
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (19 bp):
TATAAGTGGTTTGGTTTAA
Found at i:12190 original size:52 final size:52
Alignment explanation
Indices: 12112--12396 Score: 445
Period size: 52 Copynumber: 5.6 Consensus size: 52
12102 AAATGAAACG
*
12112 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
12164 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
12216 -----GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
12263 GGTCCGATGACTATATGTCATCATGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * *
12315 GGTCCAATGACTATATGTCATCGTGAGTATATGAATCCTTTATGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
12367 GGTCCGGTGACTATGTGTCATCATGAGTAT
1 GGTCCGATGACTATGTGTCATCGTGAGTAT
12397 TAAATGAAAT
Statistics
Matches: 215, Mismatches: 13, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
47 46 0.21
52 169 0.79
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:12290 original size:99 final size:100
Alignment explanation
Indices: 12117--12396 Score: 445
Period size: 99 Copynumber: 2.8 Consensus size: 100
12107 AAACGGGTCC
*
12117 GATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTATGAGGTCCGATGACTATGTGT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGT
*
12182 CATCGTGAGTATATGAATCCTTTACGGATTATGA-
66 CATCATGAGTATATGAATCCTTTACGGATTATGAG
* *
12216 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATATGT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGT
12281 CATCATGAGTATATGAATCCTTTACGGATTATGAG
66 CATCATGAGTATATGAATCCTTTACGGATTATGAG
* * * *
12316 GTCCAATGACTATATGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGTCCGGTGACTAT
1 G----ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTAT
12381 GTGTCATCATGAGTAT
62 GTGTCATCATGAGTAT
12397 TAAATGAAAT
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
99 95 0.57
100 1 0.01
104 70 0.42
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (100 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGT
CATCATGAGTATATGAATCCTTTACGGATTATGAG
Found at i:13473 original size:24 final size:25
Alignment explanation
Indices: 13449--13496 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
13439 AAACAACTTC
13449 TAAAAAAAAACTC-AAGAGCAATTCT
1 TAAAAAAAAACTCAAAGAG-AATTCT
* *
13474 TGAAGAAAAACTCAAAGAGAATT
1 TAAAAAAAAACTCAAAGAGAATT
13497 GTTTTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (25 bp):
TAAAAAAAAACTCAAAGAGAATTCT
Found at i:13723 original size:14 final size:13
Alignment explanation
Indices: 13699--13728 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
13689 TAAAAATTCG
13699 AATAAAAAATAAC
1 AATAAAAAATAAC
13712 AATAAAATAATAAC
1 AATAAAA-AATAAC
13726 AAT
1 AAT
13729 TGGTAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAAAATAAC
Found at i:17987 original size:12 final size:12
Alignment explanation
Indices: 17970--17998 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
17960 ACCTAGGGAG
17970 AGAAAAAAAAAA
1 AGAAAAAAAAAA
17982 AG-AAAAAAAAA
1 AGAAAAAAAAAA
17993 AGAAAA
1 AGAAAA
17999 TATCATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:17989 original size:11 final size:11
Alignment explanation
Indices: 17973--17998 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17963 TAGGGAGAGA
17973 AAAAAAAAAAG
1 AAAAAAAAAAG
17984 AAAAAAAAAAG
1 AAAAAAAAAAG
17995 AAAA
1 AAAA
17999 TATCATAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:19238 original size:19 final size:19
Alignment explanation
Indices: 19198--19240 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19188 CTTTTTCTAA
* *
19198 TTTTATAATATTTTTTATT
1 TTTTATAATATTTTTGACT
19217 TTTTAT-ATATTATTTGACT
1 TTTTATAATATT-TTTGACT
19236 TTTTA
1 TTTTA
19241 AAATTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTATAATATTTTTGACT
Found at i:20342 original size:13 final size:13
Alignment explanation
Indices: 20324--20349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20314 CTAATCAAAC
20324 TTAGGAGTTTAAA
1 TTAGGAGTTTAAA
20337 TTAGGAGTTTAAA
1 TTAGGAGTTTAAA
20350 GTCAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TTAGGAGTTTAAA
Found at i:21187 original size:7 final size:7
Alignment explanation
Indices: 21177--21228 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
21167 TTGTTTTTTT
21177 ACCTTGA
1 ACCTTGA
*
21184 ACCTTAA
1 ACCTTGA
*
21191 ACCCCT-A
1 A-CCTTGA
21198 ACCTTGA
1 ACCTTGA
21205 ACCTTGA
1 ACCTTGA
21212 A-CTTGA
1 ACCTTGA
*
21218 ATCTTGA
1 ACCTTGA
21225 ACCT
1 ACCT
21229 AACCCTAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 9 0.24
7 26 0.68
8 3 0.08
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (7 bp):
ACCTTGA
Found at i:27507 original size:27 final size:28
Alignment explanation
Indices: 27449--27508 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
27439 GAATAACACC
* *
27449 ACACAACAAACATATAACACAGACATAT
1 ACACAACAAACATATAACACAGACAGAG
* * *
27477 ACACAAC-AATATATAGCATAGACAGAG
1 ACACAACAAACATATAACACAGACAGAG
27504 ACACA
1 ACACA
27509 CCTCAAGTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.55, C:0.23, G:0.08, T:0.13
Consensus pattern (28 bp):
ACACAACAAACATATAACACAGACAGAG
Found at i:28853 original size:40 final size:38
Alignment explanation
Indices: 28762--28854 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 38
28752 TATTTGAATG
*
28762 TTTATTTTTTGAAATTTTCAAATGTTTAACTAGCTTTAA
1 TTTATATTTTG-AATTTTCAAATGTTTAACTAGCTTTAA
* *
28801 TTTATATATTTGAATTTTCTAAAAT-TTTAACTAGTTTTTTA
1 TTTATAT-TTTGAATTTTC--AAATGTTTAACTAG-CTTTAA
*
28842 TTTTTATTTTGAA
1 TTTATATTTTGAA
28855 AAATTAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
39 13 0.28
40 19 0.41
41 14 0.30
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.58
Consensus pattern (38 bp):
TTTATATTTTGAATTTTCAAATGTTTAACTAGCTTTAA
Done.