Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005777.1 Kokia drynarioides strain JFW-HI SEQ_120044, 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: 10614
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Found at i:723 original size:96 final size:96
Alignment explanation
Indices: 546--730 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
536 GAAGAGGATG
* ** *
546 TTCGATTATATCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGA
1 TTCGATTATATCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
*
611 AGATAAGGAAACATTGTCTCGATTAAGGGTA
66 AGATAAAGAAACATTGTCTCGATTAAGGGTA
* * **
642 TTCGATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTTCGGCGCAAATTTTC-GAAACTC
1 TTCGATTATATCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
*
706 GAA-ATAAA-AGAATATTGTCTCGATT
64 GAAGATAAAGA-AACATTGTCTCGATT
731 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.91
97 5 0.07
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (96 bp):
TTCGATTATATCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
AGATAAAGAAACATTGTCTCGATTAAGGGTA
Found at i:1150 original size:59 final size:58
Alignment explanation
Indices: 984--1210 Score: 167
Period size: 59 Copynumber: 3.9 Consensus size: 58
974 GAATTTTTAA
* * * * *
984 GGGCAAAATGGTAATTTTGGGAAAGTTTAG-GGTTAAAAATGGAATCTTTTGACATTCG
1 GGGCAAAATGGTAATTTT-TGAAAGTTTCGAGGTTAAAAATGGAATATTTGGACATCCG
* * * * * *
1042 GGG-AAGGAGGGTAA-TTTTGAGAGTTTCGAGGTTGAAAATGGAGTTTTTGGACATCCG
1 GGGCAA-AATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATATTTGGACATCCG
* * * ** *
1099 GGCGCAAAATGGTAATTTTTGAAAGTTTCGAGATCAAAAATGGAAAATTTGGAGGTTCG
1 GG-GCAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATATTTGGACATCCG
* * * * *
1158 AGGGTAAAAATGG-AATTTTT-AGAAGGTTCGGGGTCAAAAATGGAATTTTTGGA
1 -GGG-CAAAATGGTAATTTTTGA-AAGTTTCGAGGTTAAAAATGGAATATTTGGA
1211 AGTTTCGGGG
Statistics
Matches: 133, Mismatches: 28, Indels: 15
0.76 0.16 0.09
Matches are distributed among these distances:
56 8 0.06
57 30 0.23
58 17 0.13
59 69 0.52
60 9 0.07
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (58 bp):
GGGCAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATATTTGGACATCCG
Found at i:1166 original size:29 final size:29
Alignment explanation
Indices: 1104--1507 Score: 431
Period size: 29 Copynumber: 13.7 Consensus size: 29
1094 ATCCGGGCGC
* *
1104 AAAATGGTAATTTTTGAAAGTTTCGA-GATCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-A
** *
1135 AAAATGGAAAATTTGGAGGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
1164 AAAATGGAATTTTTAGAAGGTTCG-GGGTCA
1 AAAATGGAATTTTTGGAA-GTTCGAGGGT-A
1194 AAAATGGAATTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
1224 AAAATGAAATTTTTGGAAG-TCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * **
1252 AAAATGAAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
*
1282 AAAATGAAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* **
1311 AAAATAGAATTTTTGGAAGTTTTAGGGTAA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
*
1341 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* ** *
1370 AAAATAGAATTTTTGGAAGTTTTAGGGTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
** *
1399 AAAATGGAATTTTTAAAAGTT-TAGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTA
* **
1428 AATATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
1457 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1486 AAAATGGAATTTTTGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
1508 TAGGTACCTT
Statistics
Matches: 320, Mismatches: 42, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.08
29 172 0.54
30 117 0.37
31 7 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:1331 original size:59 final size:58
Alignment explanation
Indices: 1104--1508 Score: 476
Period size: 59 Copynumber: 6.9 Consensus size: 58
1094 ATCCGGGCGC
* * ** * **
1104 AAAATGGTAATTTTTGAAAGTTTCGA-GATCAAAAATGGAAAATTTGGAGGTTCGAGGGTA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTAGGGTA
* **
1164 AAAATGGAATTTTTAGAAGGTTCG-GGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAA-GTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTAGGGT-A
* * *
1224 AAAATGAAATTTTTGGAAG-TCGAGGGTAAAAATGAAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT-A
* *
1282 AAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTAA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT-A
* * *
1341 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTA
** * * *
1399 AAAATGGAATTTTTAAAAGTT-TAGGGGTAAATATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTA
*
1457 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT
1509 AGGTACCTTC
Statistics
Matches: 302, Mismatches: 35, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
58 138 0.46
59 139 0.46
60 25 0.08
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTA
Found at i:5067 original size:17 final size:17
Alignment explanation
Indices: 5045--5079 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5035 GATTTTACCT
5045 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
5062 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
5079 A
1 A
5080 TGAAAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:6279 original size:98 final size:98
Alignment explanation
Indices: 5999--6562 Score: 641
Period size: 98 Copynumber: 5.7 Consensus size: 98
5989 TCACTACAAG
* *
5999 GATATGGAAGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATGAAGCATGAAG
1 GATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC---AG-A--AA-CATGAAG
* *
6064 TGG-AAGATTTAAGCCGCAACGGCAAATCCAGTACTACGAA
59 -GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA
* *
6104 GATATGGAGGGAAAGGTTTAAG-CAGTAACAACGGCGAACCTTGTACCTCA-AGAGCATGAAGGG
1 GATATGGAAGGAAAGGTTTAAGTC-G---CAACGGCGAACCTTGTACCTCAGA-AACATGAAGGG
* * *
6167 AAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAG
61 AAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA
* ** * * *
6205 GATATGGAAGGAAAGATTTAAGTTACAATGGCGAATCTTGTACCTCAGAAGCATGAAGGGAAAGA
1 GATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
* ** *
6270 TTTAAGCCGCAACGGTGAATATAGTACCACAAA
66 TTTAAGCCGCAACGGCGAATCCAGTACCACGAA
* * *
6303 GATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAAGGAAAGA
1 GATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
* * * * *
6368 TTTAAGCGGTAATGGCAAATCCAGTATCACGAA
66 TTTAAGCCGCAACGGCGAATCCAGTACCACGAA
* * * * *
6401 GATATGGAGGGAAATGTTTAAGTCGCAACGACGAACCTTGTAGCTCAGAAACTTGAAGGGAAAGA
1 GATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
* *
6466 TTTAAGCCGCAACAGTGAATCCAGTACCACGAA
66 TTTAAGCCGCAACGGCGAATCCAGTACCACGAA
* * *
6499 GATAT-GAAGGGAAAGGTTTAAGTCGCAAAGGCAAACCTTGTACCTCAGAAACATAAAGGGAAAG
1 GATATGGAA-GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAG
6563 GTTGAGGCCG
Statistics
Matches: 392, Mismatches: 59, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
97 2 0.01
98 282 0.72
99 1 0.00
100 2 0.01
101 59 0.15
102 2 0.01
103 1 0.00
104 1 0.00
105 23 0.06
108 19 0.05
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (98 bp):
GATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
TTTAAGCCGCAACGGCGAATCCAGTACCACGAA
Found at i:6412 original size:147 final size:145
Alignment explanation
Indices: 5994--6436 Score: 356
Period size: 147 Copynumber: 2.9 Consensus size: 145
5984 TTTTATCACT
* * * *
5994 ACAAGGATATGGAAGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATGAAGCA
1 ACAAAGATAT-GAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACAT---G-A
* *
6059 TGAAGTGGAAGATTTAAGCCGCAACGGCAAATCCAGTA-CTACGAAGATATGGAGGGAAAGGTTT
61 --AAG-GAAAGATTTAAGCCGCAATGGCAAATCCAGTATC-ACGAAGATATGGAGGGAAA-GTTT
* * *
6123 AAGCAGTAACAACGGCGAACCTTGTACC
121 AAGCCG---CAACGGCGAACATAGTACC
* * * * * * * * * *
6151 TC-AAGAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-GAGGATATGGAA
1 ACAAAGA-TATG-AGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGA-AACATGAAA
*** * ** * *
6214 GGAAAGATTTAAGTTACAATGGCGAATCTTGTACCTCA-GAAG-CATGAAGGGAAAGATTTAAGC
63 GGAAAGATTTAAGCCGCAATGGCAAATCCAGTA--TCACGAAGATATGGAGGGAAAG-TTTAAGC
* *
6277 CGCAACGGTGAATATAGTACC
125 CGCAACGGCGAACATAGTACC
*
6298 ACAAAGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAAGG
1 ACAAAGATAT-GAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAAGG
* * *
6363 AAAGATTTAAGCGGTAATGGCAAATCCAGTATCACGAAGATATGGAGGGAAATGTTTAAGTCGCA
65 AAAGATTTAAGCCGCAATGGCAAATCCAGTATCACGAAGATATGGAGGGAAA-GTTTAAGCCGCA
*
6428 ACGACGAAC
129 ACGGCGAAC
6437 CTTGTAGCTC
Statistics
Matches: 220, Mismatches: 53, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
145 3 0.01
146 4 0.02
147 109 0.50
148 8 0.04
149 1 0.00
150 42 0.19
151 7 0.03
152 1 0.00
153 1 0.00
154 1 0.00
156 6 0.03
157 37 0.17
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (145 bp):
ACAAAGATATGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAAGGA
AAGATTTAAGCCGCAATGGCAAATCCAGTATCACGAAGATATGGAGGGAAAGTTTAAGCCGCAAC
GGCGAACATAGTACC
Found at i:6542 original size:49 final size:49
Alignment explanation
Indices: 6058--6542 Score: 330
Period size: 49 Copynumber: 9.8 Consensus size: 49
6048 AGCATGAAGC
* *
6058 ATGAAGTGG-AAGATTTAAGCCGCAACGGCAAATCC-AGTACTACGAAGAT
1 ATGAAG-GGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCACGAAGAT
* * * * * *
6107 ATGGAGGGAAAGGTTTAAGCAGTAACAACGGCGAACCTTGTACCTC-AAGAGC
1 ATGAAGGGAAAGATTTAAGCCG---CAACGGCGAACCTAGTACCACGAAGA-T
* * *
6159 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAGGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACGAAGAT
*** * * * * *
6208 ATGGAA-GGAAAGATTTAAGTTACAATGGCGAATCTTGTACCTCAGAAG-C
1 AT-GAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCAC-GAAGAT
* ** *
6257 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAATATAGTACCACAAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACGAAGAT
* * * * *
6306 AT-AGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-AC
1 ATGA-AGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCAC-GAAGAT
* * * * * *
6355 ATGAAAGGAAAGATTTAAGCGGTAATGGCAAATCC-AGTATCACGAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCACGAAGAT
* * * *
6404 ATGGAGGGAAATG-TTTAAGTCGCAACGACGAACCTTGTAGCTCA-GAA-ACT
1 ATGAAGGGAAA-GATTTAAGCCGCAACGGCGAACCTAGTA-C-CACGAAGA-T
* *
6454 -TGAAGGGAAAGATTTAAGCCGCAACAGTGAATCC-AGTACCACGAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCACGAAGAT
* * * * *
6502 ATGAAGGGAAAGGTTTAAGTCGCAAAGGCAAACCTTGTACC
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACC
6543 TCAGAAACAT
Statistics
Matches: 330, Mismatches: 79, Indels: 54
0.71 0.17 0.12
Matches are distributed among these distances:
47 2 0.01
48 22 0.07
49 244 0.74
50 21 0.06
51 8 0.02
52 33 0.10
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (49 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACGAAGAT
Found at i:9745 original size:19 final size:19
Alignment explanation
Indices: 9721--9784 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
9711 ATTAAATAGG
9721 ATTTAAATAAATATTTTTA
1 ATTTAAATAAATATTTTTA
*
9740 ATTTAATTCAAATA-TTTTA
1 ATTTAAAT-AAATATTTTTA
9759 TATATT-AAT-AATATTTTT-
1 -AT-TTAAATAAATATTTTTA
9777 ATTTAAAT
1 ATTTAAAT
9785 TTAATTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
16 2 0.05
17 5 0.13
18 4 0.11
19 16 0.42
20 9 0.24
21 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAATAAATATTTTTA
Found at i:9789 original size:19 final size:17
Alignment explanation
Indices: 9721--9782 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 17
9711 ATTAAATAGG
9721 ATTTAAATAAATATTTTT
1 ATTT-AATAAATATTTTT
9739 AATTTAATTCAAATATTTTAT
1 -ATTTAA-T-AAATATTTT-T
9760 ATATTAAT-AATATTTTT
1 AT-TTAATAAATATTTTT
9777 ATTTAA
1 ATTTAA
9783 ATTTAATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.10
17 3 0.08
18 10 0.26
19 5 0.13
20 12 0.31
21 5 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTAATAAATATTTTT
Done.