Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001161.1 Kokia drynarioides strain JFW-HI SEQ_112482, 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: 89511
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:1298 original size:17 final size:17
Alignment explanation
Indices: 1276--1318 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
1266 TGTGGGAAAG
1276 GGGTTTTAGTTTAGAGA
1 GGGTTTTAGTTTAGAGA
1293 GGGTTTTAGTTTAGAGA
1 GGGTTTTAGTTTAGAGA
1310 GGGTTTTAG
1 GGGTTTTAG
1319 ATTGGGGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (17 bp):
GGGTTTTAGTTTAGAGA
Found at i:5459 original size:18 final size:19
Alignment explanation
Indices: 5432--5467 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5422 GTTTTTTTAA
*
5432 TAAAATAAAATA-AAAAAT
1 TAAAAGAAAATAGAAAAAT
5450 TAAAAGAAAATAGAAAAA
1 TAAAAGAAAATAGAAAAA
5468 AATCATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
TAAAAGAAAATAGAAAAAT
Found at i:9399 original size:13 final size:13
Alignment explanation
Indices: 9381--9407 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9371 CACCATTGAC
9381 TTGTAACTTTATT
1 TTGTAACTTTATT
9394 TTGTAACTTTATT
1 TTGTAACTTTATT
9407 T
1 T
9408 ATACCCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTGTAACTTTATT
Found at i:17585 original size:285 final size:273
Alignment explanation
Indices: 17072--18183 Score: 1254
Period size: 285 Copynumber: 4.0 Consensus size: 273
17062 TAAATCCCAA
* * * *
17072 AAGTATAATTGGTGCATAACAATATAGATTAGCCGTCAGGTTAGCAATTTAAACCCTAATAAAAA
1 AAGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCC---TAAAAA
* *
17137 AACTCATAAAGGTCAATCCTTTTTTTCACAATCTTCGATCCCTCATTCAAA-CAGATCTCCTAAA
63 AATTCATAAAGGTCAATCCTTTTTTTCACATTCTTCGATCCCTCATTCAAACCA-ATCTCCTAAA
* * * * * *
17201 CCCCAAAACTAATAAATCCCCATTAAAGATGTACCAGAAAAAAACAATTAATTTGAACTTAAATC
127 CCCC-AAACTAATAAA-ACCCATTAAACAAGTA-CAAAAAAAAACAATTACTTTGAACTTAAAAC
* * * *
17266 ACTTAAAAAAATCAAATTAGAACCATTAAAAGAACAAACTTTAAAGCAAAATACCTCAAAGGTCT
189 ACTGAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGAGGGTCT
* * *
17331 GATTGGAGTAGTAGATGGAG
254 GATTGGAGGAGTGGATGAAG
* * * *
17351 AAGTGTAACTGGTGCATAACAAAAAAAATTAACAGTCAGGTTAACAATTTAAACCCTAACAAAAA
1 AAGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCT------AA
* *
17416 AAATAATTCGTAAAGGTAAATCC-TTTTTTCACATTCTTCGATCCCTCATTCATGCAACCAATCT
60 AAA-AATTCATAAAGGTCAATCCTTTTTTTCACATTCTTCGATCCCTCATTCA---AACCAATCT
* * * *
17480 CCTACATCCCAAACTAATAAAACCCATTAAACAAGAACCAAACAAAAACCCAATTACTTTGAACT
121 CCTAAACCCCAAACTAATAAAACCCATTAAACAAGTA-CAAA-AAAAA-ACAATTACTTTGAACT
*
17545 TAAAACACTGAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTTAAGCAAAATACCTCGA
183 TAAAACACTGAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGA
*
17610 GGGTCTGATTGGAGGAGTGGATAAAG
248 GGGTCTGATTGGAGGAGTGGATGAAG
*
17636 GAGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCT------A-
1 AAGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCTAAAAAAAT
* *
17694 --AT-AA--T---T-CTTTTTTTCACATTCTTCGATCCCTCATTCAAATCAATCTCCTACACCCC
66 TCATAAAGGTCAATCCTTTTTTTCACATTCTTCGATCCCTCATTCAAACCAATCTCCTAAACCCC
17750 AAACTAATACAAACCCATTAAACAAGTACAAAAAACAAACAATTACTTTGAACTTAAAAGTTAAA
131 AAACTAATA-AAACCCATTAAACAAGTACAAAAAA-AAACAATTACTTTGAAC-------TTAAA
* * *
17815 ACACTGAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAAAACCTGGAGGGC
187 ACACTGAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGAGGGT
17880 CTGATTGGAGGAGTGGATGAAG
252 CTGATTGGAGGAGTGGATGAAG
* * *
17902 GAGTATAACTGGTGCATAACAAAATAAACTAGCGGTCAGGTTAGCAATTTAAACCCTAACAAAAA
1 AAGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCT-A-AAAAA
** * *
17967 AACCATAAAAGTCAATCCTTTTTTTCACAGTCTTCGATCCCTCATTCAATACAACCAATCTCCTA
64 ATTCATAAAGGTCAATCCTTTTTTTCACATTCTTCGATCCCTCATTC---A-AACCAATCTCCTA
* * **
18032 AACCCCAAACTAATGAAAACCCATTAAAGAAGTACAAAAAAAAAAAATTACTTCAAACTT-AAAC
125 AACCCCAAACTAAT-AAAACCCATTAAACAAGTACAAAAAAAAACAATTACTTTGAACTTAAAAC
* * * *
18096 ACTGAAAAACAAAATCAAATTAGAACCGTTAAAAGAACAAGCATTAAAGCAAAATACCTTGGGGG
189 ACTG--AAA-AAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGAGGG
* *
18161 CCTGATTGGAGGAGCGGATGAAG
251 TCTGATTGGAGGAGTGGATGAAG
18184 GAGGAGGAGG
Statistics
Matches: 723, Mismatches: 61, Indels: 95
0.82 0.07 0.11
Matches are distributed among these distances:
259 17 0.02
260 32 0.04
261 17 0.02
262 1 0.00
263 30 0.04
266 143 0.20
268 2 0.00
269 1 0.00
272 1 0.00
274 1 0.00
276 1 0.00
277 2 0.00
278 2 0.00
279 56 0.08
280 3 0.00
281 3 0.00
282 105 0.15
283 33 0.05
284 45 0.06
285 161 0.22
286 2 0.00
287 15 0.02
288 49 0.07
289 1 0.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (273 bp):
AAGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCTAAAAAAAT
TCATAAAGGTCAATCCTTTTTTTCACATTCTTCGATCCCTCATTCAAACCAATCTCCTAAACCCC
AAACTAATAAAACCCATTAAACAAGTACAAAAAAAAACAATTACTTTGAACTTAAAACACTGAAA
AAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGAGGGTCTGATTGGA
GGAGTGGATGAAG
Found at i:23064 original size:11 final size:11
Alignment explanation
Indices: 23034--23089 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
23024 ACGTTTAATG
*
23034 TAAAATAAACA
1 TAAAATAAAAA
23045 TAAACATAAAAA
1 TAAA-ATAAAAA
23057 TAAAAT-AAAA
1 TAAAATAAAAA
23067 TAAAA-ACAAAA
1 TAAAATA-AAAA
* *
23078 CAAAACAAAAA
1 TAAAATAAAAA
23089 T
1 T
23090 CCAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 9 0.24
11 18 0.47
12 11 0.29
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:31277 original size:24 final size:28
Alignment explanation
Indices: 31238--31291 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
31228 AAAATATAAG
31238 AATTGTTTAAAAATTAATT-TTT-TTAA
1 AATTGTTTAAAAATTAATTATTTATTAA
*
31264 AATT-TTT-AAAATTATTTATTTATTAA
1 AATTGTTTAAAAATTAATTATTTATTAA
31290 AA
1 AA
31292 GTCGCCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 6 0.24
26 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
AATTGTTTAAAAATTAATTATTTATTAA
Found at i:34873 original size:5 final size:5
Alignment explanation
Indices: 34863--34888 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34853 GGATTTTGAT
34863 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
34889 CATCAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:35615 original size:17 final size:16
Alignment explanation
Indices: 35593--35655 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
35583 TTTATTTTTT
35593 AAAATTTTAAAGATTAA
1 AAAATTTTAAA-ATTAA
*
35610 AAAA--TTAAAATTTA
1 AAAATTTTAAAATTAA
35624 AAAATTATTAAAATTATA
1 AAAATT-TTAAAATTA-A
35642 TAAAATTTATAAAA
1 -AAAATTT-TAAAA
35656 AAAAAAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
17 12 0.32
18 2 0.05
19 11 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AAAATTTTAAAATTAA
Found at i:35617 original size:23 final size:23
Alignment explanation
Indices: 35591--35639 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
35581 AATTTATTTT
*
35591 TTAAAATTTTAAAGATTA-AAAAA
1 TTAAAA-TTTAAAAATTATAAAAA
*
35614 TTAAAATTTAAAAATTATTAAAA
1 TTAAAATTTAAAAATTATAAAAA
35637 TTA
1 TTA
35640 TATAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAAAATTTAAAAATTATAAAAA
Found at i:35652 original size:9 final size:9
Alignment explanation
Indices: 35615--35655 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
35605 ATTAAAAAAT
35615 TAAAATTTA
1 TAAAATTTA
35624 -AAAA-TTA
1 TAAAATTTA
35631 TTAAAATTATA
1 -TAAAATT-TA
35642 TAAAATTTA
1 TAAAATTTA
35651 TAAAA
1 TAAAA
35656 AAAAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.11
8 4 0.14
9 11 0.39
10 8 0.29
11 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TAAAATTTA
Found at i:43397 original size:14 final size:14
Alignment explanation
Indices: 43373--43416 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
43363 CATATATACA
43373 CACACTCATATTTG
1 CACACTCATATTTG
* * *
43387 CATACTTATATATG
1 CACACTCATATTTG
*
43401 TACACTCATATTTG
1 CACACTCATATTTG
43415 CA
1 CA
43417 GCATTTATTA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (14 bp):
CACACTCATATTTG
Found at i:46162 original size:64 final size:64
Alignment explanation
Indices: 46061--46188 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
46051 TATGTCCTCC
46061 AACAACATACACATTCTGTAATTATAGTAAGTAAAAAAAAATCTTAATATCACTCGACACGGCA
1 AACAACATACACATTCTGTAATTATAGTAAGTAAAAAAAAATCTTAATATCACTCGACACGGCA
46125 AACAACATACACATTCTGTAATTATAGTAAGTAAAAAAAAATCTTAATATCACTCGACACGGCA
1 AACAACATACACATTCTGTAATTATAGTAAGTAAAAAAAAATCTTAATATCACTCGACACGGCA
46189 TATAACTATC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (64 bp):
AACAACATACACATTCTGTAATTATAGTAAGTAAAAAAAAATCTTAATATCACTCGACACGGCA
Found at i:58611 original size:138 final size:136
Alignment explanation
Indices: 58230--58683 Score: 506
Period size: 138 Copynumber: 3.3 Consensus size: 136
58220 TTAATATTTG
* * * * *
58230 TGATTGATTATC-GATTGGGGTGATTAACGTCTATGTTACACGACTTGGGTTTGTTTTTATTTCA
1 TGATTGATTACCAG-TTGGAGTGATTAATGTCTATGTTACTCGACTTGGGTTTGTTTTTCTTTCA
* * * *
58294 AAAACGT--TGTCATAGCCGAACCTCATAGTGTAGGGACTAGGGTGCTACACTTGTAAACCTACG
65 AAAAAGTAATGTCATAGCCGAACCTCATAGTTTTGGGACTAGGGTGTTACACTTGTAAACCTACG
*
58357 GAATTGG
130 GAATTGA
* * * * * *
58364 TGATTGATTACCGGTT-GAGTAATCAATATTTGTGATTGATTACTCGATTTGGGTTTGTTTTTCT
1 TGATTGATTACCAGTTGGAGTGAT-TA-ATGTCT-A-TG-TTACTCGACTTGGGTTTGTTTTTCT
* * *
58428 TTCAAAAAAGTTATATGTCATAGCCAAACCTCATAGTTTTCGGACTAGGGTGTTAGACTTGTAAA
61 TTCAAAAAAG-TA-ATGTCATAGCCGAACCTCATAGTTTTGGGACTAGGGTGTTACACTTGTAAA
58493 CCTACGGAATTGA
124 CCTACGGAATTGA
* * **
58506 TGATTGATTACCAGTTGGGGTGATTAATGTCTATGTTACTCGACTCGGGTTTGTTTTTCTTTTGA
1 TGATTGATTACCAGTTGGAGTGATTAATGTCTATGTTACTCGACTTGGGTTTGTTTTTCTTTCAA
* * * *
58571 AAAGGATACATGTCATAGCGGAACCTCGTAGTTTTGGGACTA-GG-GTTACACTTGTAAAACTAC
66 AAAAG-TA-ATGTCATAGCCGAACCTCATAGTTTTGGGACTAGGGTGTTACACTTGTAAACCTAC
*
58634 AGAATTGA
129 GGAATTGA
* *
58642 TGATTGATTACCAATTGGAGTGATTAATGTCTATGCTACTCG
1 TGATTGATTACCAGTTGGAGTGATTAATGTCTATGTTACTCG
58684 GATTTGTTCT
Statistics
Matches: 268, Mismatches: 41, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
133 5 0.02
134 14 0.05
135 4 0.01
136 64 0.24
137 4 0.01
138 92 0.34
139 3 0.01
140 1 0.00
141 4 0.01
142 72 0.27
143 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (136 bp):
TGATTGATTACCAGTTGGAGTGATTAATGTCTATGTTACTCGACTTGGGTTTGTTTTTCTTTCAA
AAAAGTAATGTCATAGCCGAACCTCATAGTTTTGGGACTAGGGTGTTACACTTGTAAACCTACGG
AATTGA
Found at i:65438 original size:25 final size:25
Alignment explanation
Indices: 65404--65455 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
65394 CTAAACCCTT
65404 ACCACATATAAACCCCTAGGATCTA
1 ACCACATATAAACCCCTAGGATCTA
65429 ACCACATATAAACCCCTAGGATCTA
1 ACCACATATAAACCCCTAGGATCTA
65454 AC
1 AC
65456 TAGAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.33, G:0.08, T:0.19
Consensus pattern (25 bp):
ACCACATATAAACCCCTAGGATCTA
Found at i:76382 original size:22 final size:23
Alignment explanation
Indices: 76354--76400 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
76344 ATGATCTAAA
76354 ACTTGTTAAATAA-TTATTGAAT
1 ACTTGTTAAATAACTTATTGAAT
76376 ACTTGTTAAATAACTTATTGAAT
1 ACTTGTTAAATAACTTATTGAAT
76399 AC
1 AC
76401 GATGCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (23 bp):
ACTTGTTAAATAACTTATTGAAT
Found at i:88671 original size:16 final size:16
Alignment explanation
Indices: 88640--88676 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
88630 ATGTGAATAA
88640 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
88656 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
88672 TATTA
1 TATTA
88677 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:88742 original size:25 final size:26
Alignment explanation
Indices: 88705--88765 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
88695 AAATAATTTA
* *
88705 AAATAATTAATTATATTAAT-TATAT
1 AAATAATTAATTATATGAATAAATAT
* *
88730 TAATAATTTATTATATGAATAAATAT
1 AAATAATTAATTATATGAATAAATAT
88756 AAATAATTAA
1 AAATAATTAA
88766 ATATGTATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AAATAATTAATTATATGAATAAATAT
Found at i:88794 original size:13 final size:13
Alignment explanation
Indices: 88778--88822 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
88768 ATGTATGTTT
88778 AATATTATTGAAA
1 AATATTATTGAAA
*
88791 AATA-TATTCAAAAA
1 AATATTATT--GAAA
88805 AATATTATTGAAA
1 AATATTATTGAAA
88818 AATAT
1 AATAT
88823 AATATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
14 7 0.26
15 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (13 bp):
AATATTATTGAAA
Done.