Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014210.1 Kokia drynarioides strain JFW-HI SEQ_129243, 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: 46294
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:5671 original size:20 final size:21
Alignment explanation
Indices: 5646--5685 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5636 TAATTTTTAA
5646 ATATTAAAATAA-TATTATTT
1 ATATTAAAATAATTATTATTT
*
5666 ATATTAATATAATTATTATT
1 ATATTAAAATAATTATTATT
5686 AATTTTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTAAAATAATTATTATTT
Found at i:7937 original size:2 final size:2
Alignment explanation
Indices: 7930--7964 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7920 ACTAATGTTA
7930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7965 ATGTTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9326 original size:19 final size:19
Alignment explanation
Indices: 9299--9349 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
9289 TGGCAAAAAT
* *
9299 AACAATAAAACAACACCA-A
1 AACAGTAAAA-AAAACCAGA
9318 AACAGTAAAAAAAACCAGA
1 AACAGTAAAAAAAACCAGA
*
9337 AAGAGTAAAAAAA
1 AACAGTAAAAAAA
9350 TAGAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.71, C:0.16, G:0.08, T:0.06
Consensus pattern (19 bp):
AACAGTAAAAAAAACCAGA
Found at i:11996 original size:2 final size:2
Alignment explanation
Indices: 11989--12016 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11979 TTTTCTTTCT
11989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12017 ACATTCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16651 original size:20 final size:19
Alignment explanation
Indices: 16611--16651 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
16601 AAAGAAAACC
16611 TAAAATATTTTTTTATGAA
1 TAAAATATTTTTTTATGAA
16630 TAAATATATTATTTTTAT-AA
1 TAAA-ATATT-TTTTTATGAA
16650 TA
1 TA
16652 TATAGCATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TAAAATATTTTTTTATGAA
Found at i:19322 original size:27 final size:27
Alignment explanation
Indices: 19265--19322 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
19255 AAAATTATGG
* *
19265 GATT-AAAGATTAAATTTAAAAAAAGA
1 GATTAAAACATTAAATGTAAAAAAAGA
*
19291 CATTAAAACATTAAATGTAAGAAAAA-A
1 GATTAAAACATTAAATGTAA-AAAAAGA
19318 GATTA
1 GATTA
19323 TTGTTAGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 3 0.12
27 18 0.69
28 5 0.19
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.26
Consensus pattern (27 bp):
GATTAAAACATTAAATGTAAAAAAAGA
Found at i:20709 original size:32 final size:31
Alignment explanation
Indices: 20672--20749 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 31
20662 TAAAATGAAT
*
20672 CCAAAATATTATTTTTTTAGTTGTTAAGCGGC
1 CCAAAATATTATTTTTTTAGTTGTTAAG-AGC
* * *
20704 CCAAAAAAATATTTTTTTAGTTTTTAAGAGC
1 CCAAAATATTATTTTTTTAGTTGTTAAGAGC
20735 CCAAAATATT-TTTTT
1 CCAAAATATTATTTTT
20750 ACTAACTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 5 0.12
31 10 0.25
32 25 0.62
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (31 bp):
CCAAAATATTATTTTTTTAGTTGTTAAGAGC
Found at i:23397 original size:42 final size:43
Alignment explanation
Indices: 23330--23410 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 43
23320 AAACTTGCAC
23330 GAGAAAAATATTTAATATGAGCTACAATCAAATCAATATAATA
1 GAGAAAAATATTTAATATGAGCTACAATCAAATCAATATAATA
*
23373 GAGATAAATATTTAATATG-GCTACAATCAAATCAATAT
1 GAGAAAAATATTTAATATGAGCTACAATCAAATCAATAT
23411 TTGTATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 19 0.51
43 18 0.49
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (43 bp):
GAGAAAAATATTTAATATGAGCTACAATCAAATCAATATAATA
Found at i:25852 original size:31 final size:31
Alignment explanation
Indices: 25815--25875 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
25805 TTATAATTTT
* *
25815 CAAGTTCAGGGA-CTAAAATGAACTTAGTTGC
1 CAAGTTCAAGGATC-AAAATGAACCTAGTTGC
*
25846 CAAGTTCAAGTATCAAAATGAACCTAGTTG
1 CAAGTTCAAGGATCAAAATGAACCTAGTTG
25876 TGAAGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (31 bp):
CAAGTTCAAGGATCAAAATGAACCTAGTTGC
Found at i:27022 original size:174 final size:172
Alignment explanation
Indices: 26728--27055 Score: 446
Period size: 174 Copynumber: 1.9 Consensus size: 172
26718 AAAACCTATA
* * *
26728 GTTTAGATAATTCCAGACACTCCATTTATAGTAGGAGAAAACACGCTATAGAGGGCATGACTTAT
1 GTTTAAATAATTCCAGACACTCCATTTATAGTAGGAGAAAACAAGCTATAGAGGGCATAACTTAT
* * * *
26793 CTTCTTCTTTTTCAAAAAGTCTTCTATCTCCCAGCTCCAAAACCTTCTTCAAGACCA-TCCTATC
66 CTTCTTCTTCTTCAAAAAATCTTCTATCTCCCAACTCCAAAACCTTCTCCAAGACCACT-CTATC
26857 TTCCCTTTTTTCAC-TTCTGTTGATATTATGTATCAACAACATG
130 TTCCCTTTTTTCACTTTC-GTTGATATTATGTATCAACAACATG
* * * *
26900 GTTTAAATAATTCCAGACACTCCATTTATGGTATGAGAGAAGATAATCTGA-AGAGGGCATAACT
1 GTTTAAATAATTCCAGACACTCCATTTATAGTA-G-GAGAAAACAAGCT-ATAGAGGGCATAACT
* * * * *
26964 TATCTTCTTCTTCTTCAAAAAATCTTCTGTCTCCTAACTTCAAATCCTTCTCCAAGACCACTTTA
63 TATCTTCTTCTTCTTCAAAAAATCTTCTATCTCCCAACTCCAAAACCTTCTCCAAGACCACTCTA
27029 TCTTCCCTTTTTTCACTTTCGTTGATA
128 TCTTCCCTTTTTTCACTTTCGTTGATA
27056 ATGTATATCA
Statistics
Matches: 135, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
172 31 0.23
173 1 0.01
174 98 0.73
175 5 0.04
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (172 bp):
GTTTAAATAATTCCAGACACTCCATTTATAGTAGGAGAAAACAAGCTATAGAGGGCATAACTTAT
CTTCTTCTTCTTCAAAAAATCTTCTATCTCCCAACTCCAAAACCTTCTCCAAGACCACTCTATCT
TCCCTTTTTTCACTTTCGTTGATATTATGTATCAACAACATG
Found at i:29390 original size:20 final size:20
Alignment explanation
Indices: 29338--29393 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
29328 TCAACAAAAA
* *
29338 TCAAAGTATCGATACTCTTG
1 TCAAAGTATTGATACTCTTC
* * * *
29358 TCAAAATACTGATATTTTTC
1 TCAAAGTATTGATACTCTTC
29378 TCAAAGTATTGATACT
1 TCAAAGTATTGATACT
29394 TTGTATGAGG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
TCAAAGTATTGATACTCTTC
Found at i:33178 original size:62 final size:62
Alignment explanation
Indices: 33112--33238 Score: 143
Period size: 61 Copynumber: 2.1 Consensus size: 62
33102 ACATTCTATT
* **
33112 TTTTTTA-TCCTAAATAT-AAAAAATTCAACAAACTTAGCCCTCAATGTTTACAAAATTTGTCA
1 TTTTTTAGT-CTAAAT-TCAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCA
* * * * *
33174 -TTTTTAGTTTGAATTCAAAAAAATCAATAAATTTAGCCCTCAACATTTACAAAATTTTTCA
1 TTTTTTAGTCTAAATTCAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCA
33235 TTTT
1 TTTT
33239 AATTTGAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
60 1 0.02
61 49 0.91
62 4 0.07
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (62 bp):
TTTTTTAGTCTAAATTCAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCA
Found at i:33210 original size:61 final size:61
Alignment explanation
Indices: 33128--33257 Score: 172
Period size: 61 Copynumber: 2.1 Consensus size: 61
33118 ATCCTAAATA
* ** * *
33128 TAAAAAATTCAACAAACTTAGCCCTCAATGTTTACAAAATTTGTCATTTTTAGTTTGAATTC
1 TAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCA-TTTTAATTTGAATCC
* * *
33190 -AAAAAAATCAATAAATTTAGCCCTCAACATTTACAAAATTTTTCATTTTAATTTGAATCC
1 TAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCATTTTAATTTGAATCC
33250 TAAAAAAA
1 TAAAAAAA
33258 ATTAATTCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
60 13 0.22
61 46 0.78
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.36
Consensus pattern (61 bp):
TAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCATTTTAATTTGAATCC
Found at i:33393 original size:51 final size:51
Alignment explanation
Indices: 33284--33393 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
33274 TATTATTTAT
* * * *
33284 TTAGAATTCGAATTAAAATGATAATTTTCATAAACATTGATGGTAATTTTT
1 TTAGAATTCAAATTAAAATGATAATTTTCATAAACATTGAGGGTAAATTTG
* *
33335 TTAGAATTCAAATTAAAATGATTAATTTT-GTAAATATTGAGGGCTAAATTTG
1 TTAGAATTCAAATTAAAATGA-TAATTTTCATAAACATTGAGGG-TAAATTTG
33387 TT-GAATT
1 TTAGAATT
33394 TTTTATATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
51 36 0.71
52 15 0.29
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (51 bp):
TTAGAATTCAAATTAAAATGATAATTTTCATAAACATTGAGGGTAAATTTG
Found at i:36279 original size:6 final size:6
Alignment explanation
Indices: 36263--36298 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
36253 GGCTTTGGTG
*
36263 GAAGG- GAAGGA GAAGGA GAAGGA GAAGGA GGAGGA G
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA G
36299 CAGAAGCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:39019 original size:16 final size:16
Alignment explanation
Indices: 38998--39067 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
38988 TTTGGTTCGC
38998 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
* *
39014 TGTAATGGAATAAAGC
1 TGTAATGGAATAGAGT
*
39030 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
*
39046 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
39062 TGTAAT
1 TGTAAT
39068 CAGTAATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.36, C:0.01, G:0.31, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:39067 original size:32 final size:32
Alignment explanation
Indices: 38996--39057 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
38986 CGTTTGGTTC
38996 GCTGTAATGGAATAGAGTTGTAATGGAATAAA
1 GCTGTAATGGAATAGAGTTGTAATGGAATAAA
*
39028 GCTGTAATGGAATAGGGTTGTAATGGAATA
1 GCTGTAATGGAATAGAGTTGTAATGGAATA
39058 GGGTTGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.03, G:0.31, T:0.29
Consensus pattern (32 bp):
GCTGTAATGGAATAGAGTTGTAATGGAATAAA
Found at i:39301 original size:58 final size:56
Alignment explanation
Indices: 39239--39361 Score: 176
Period size: 58 Copynumber: 2.2 Consensus size: 56
39229 TTTTAATAAG
* * *
39239 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATAAAATTTAATAAAAAT-AT--ATAATTTAATAACATTTTTAACATA
*
39297 ATTATTATTAAATAAAATTTAATAAAAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATAAAATTTAATAAAAATATATAATTTAATAACATTTTTAACATA
39353 ATTATTATT
1 ATTATTATT
39362 TTATTAAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 12 0.20
56 18 0.30
57 2 0.03
58 28 0.47
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (56 bp):
ATTATTATTAAATAAAATTTAATAAAAATATATAATTTAATAACATTTTTAACATA
Found at i:39398 original size:27 final size:27
Alignment explanation
Indices: 39276--39403 Score: 93
Period size: 26 Copynumber: 4.7 Consensus size: 27
39266 ATAATAAATA
* * * *
39276 ATTTAATTATATTTTAACATAATTATT
1 ATTTAAATAAATTTTAATAGAATTATT
* * *
39303 A-TTAAATAAAATTTAATAAAAATATATA
1 ATTTAAATAAATTTTAAT-AGAAT-TATT
*
39331 ATTT-AATAACATTTTTAATATAATTATT
1 ATTTAAATAA-A-TTTTAATAGAATTATT
* *
39359 ATTTTATTAAATTTTAATAGAATTATT
1 ATTTAAATAAATTTTAATAGAATTATT
39386 -TTTAAATATAA-TTTAATA
1 ATTTAAATA-AATTTTAATA
39404 ATAATTATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
26 25 0.31
27 22 0.27
28 17 0.21
29 11 0.14
30 6 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (27 bp):
ATTTAAATAAATTTTAATAGAATTATT
Found at i:40991 original size:51 final size:51
Alignment explanation
Indices: 40923--41094 Score: 265
Period size: 51 Copynumber: 3.4 Consensus size: 51
40913 AGGTCTGATA
* **
40923 ACTAAATGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCTGATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCAATG
* *
40974 ACTAACTGTCATTGTGAGTAAATGAATCCTTTATGGATTAATA-GTCCAATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAA-AGGTCCAATG
* *
41025 ACTAAGTGTTATCGTGAGTAAATGAATCCTTTATGGGTTAAAGGTCCAATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCAATG
41076 ACTAAGTGTCATCGTGAGT
1 ACTAAGTGTCATCGTGAGT
41095 TTATAGATTC
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
50 1 0.01
51 108 0.98
52 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (51 bp):
ACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCAATG
Found at i:43262 original size:30 final size:30
Alignment explanation
Indices: 43228--43292 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
43218 ACTTATTTTA
* * * *
43228 TTGTTACTTTTGTTATTATTATAGAGGTAT
1 TTGTTAATTTTGTTACTATTATAAAGGCAT
*
43258 TTGTTAATTTTGTTACTATTTTAAAGGCAT
1 TTGTTAATTTTGTTACTATTATAAAGGCAT
43288 TTGTT
1 TTGTT
43293 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTATAAAGGCAT
Done.