Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013964.1 Kokia drynarioides strain JFW-HI SEQ_128995, 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: 26044
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:8839 original size:59 final size:58
Alignment explanation
Indices: 8745--9086 Score: 313
Period size: 59 Copynumber: 5.8 Consensus size: 58
8735 ATGCACGGGG
* * *
8745 CAAAATGGTAATTTTGGGAAATTTCG-GGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 CAAAATGG-AATTTTTGG-AAGTTCGAGGG-TAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * *
8805 -AAAATGGTAATTTTTGGAAGTTTTG-GGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 CAAAATGG-AATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTGAGGGT
* * *
8864 -GAAATGGTAATTTTTGGAAGTTCGAGGGT-GAAATGGTAATTTTTGGAAGTTTCAGGGT
1 CAAAATGG-AATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTTGGAAGTTTGAGGGT
* * * *
8922 CAAAATTGGGATTTTTGGAAGTTCGAGGGTGAAAA-GTAATTTTTTTGGAAGTTTTAGGGT
1 CAAAA-TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAA--TTTTTGGAAGTTTGAGGGT
* * *
8982 CAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATTGTAATTTTTTGGAAGTTTTG-GGGT
1 C-AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAG-TTTGAGGGT
* *
9042 CAAAAATGGGATTTTTGGAAGTTCAAGGGT-AAAATGGTAATTTTT
1 C-AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTT
9087 AGACAATCTA
Statistics
Matches: 246, Mismatches: 23, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
57 6 0.02
58 25 0.10
59 106 0.43
60 98 0.40
61 11 0.04
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.37
Consensus pattern (58 bp):
CAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:8850 original size:30 final size:29
Alignment explanation
Indices: 8746--9086 Score: 254
Period size: 30 Copynumber: 11.5 Consensus size: 29
8736 TGCACGGGGC
* *
8746 AAAATGGTAATTTTGGGAAATTTCGGGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGG-TA
*
8777 AAAATGGGATTTTTGGAAGTTT-GAGGGT-
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
8805 AAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGT-A
*
8836 AAAATGGGATTTTTGGAAG-TTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
*
8864 GAAATGGTAATTTTTGGAAG-TTCGAGGGT-
1 AAAATGG-AATTTTTGGAAGTTTCG-GGGTA
* *
8893 GAAATGGTAATTTTTGGAAGTTTCAGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGT-A
* * *
8924 AAATTGGGATTTTTGGAAG-TTCGAGGGTG
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* **
8953 AAAA-GTAATTTTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAA--TTTTTGGAAGTTTCGGGGT-A
*
8984 AAAATGGGATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* * *
9013 AAATTGTAATTTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAA-TTTTTGGAAGTTTCGGGGT-A
* *
9044 AAAATGGGATTTTTGGAAG-TTCAAGGGT-
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
9072 AAAATGGTAATTTTT
1 AAAATGG-AATTTTT
9087 AGACAATCTA
Statistics
Matches: 253, Mismatches: 34, Indels: 48
0.76 0.10 0.14
Matches are distributed among these distances:
28 23 0.09
29 87 0.34
30 106 0.42
31 35 0.14
32 2 0.01
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:8993 original size:60 final size:59
Alignment explanation
Indices: 8873--9086 Score: 324
Period size: 60 Copynumber: 3.6 Consensus size: 59
8863 TGAAATGGTA
* * *
8873 ATTTTTGGAAGTTCGAGGGTGAAATGGTAA-TTTTTGGAAGTTTCAGGGTCAAAATTGGG
1 ATTTTTGGAAGTTCGAGGGTAAAAT-GTAATTTTTTGGAAGTTTTAGGGTCAAAAATGGG
8932 ATTTTTGGAAGTTCGAGGGTGAAAA-GTAATTTTTTTGGAAGTTTTAGGGTCAAAAATGGG
1 ATTTTTGGAAGTTCGAGGGT-AAAATGTAA-TTTTTTGGAAGTTTTAGGGTCAAAAATGGG
*
8992 ATTTTTGGAAGTTCGAGGGTAAAATTGTAATTTTTTGGAAGTTTTGGGGTCAAAAATGGG
1 ATTTTTGGAAGTTCGAGGGTAAAA-TGTAATTTTTTGGAAGTTTTAGGGTCAAAAATGGG
*
9052 ATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTT
1 ATTTTTGGAAGTTCGAGGGTAAAAT-GTAATTTTT
9087 AGACAATCTA
Statistics
Matches: 144, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
58 4 0.03
59 25 0.17
60 111 0.77
61 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (59 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTTGGAAGTTTTAGGGTCAAAAATGGG
Found at i:9964 original size:23 final size:22
Alignment explanation
Indices: 9916--9965 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
9906 TCAAACCCGT
* *
9916 TTTTTTTTAAACGTTTTCCCCT
1 TTTTTTTTAAACGTTTTACCCA
**
9938 TTTTTTTTAAACCGTTTTATTCA
1 TTTTTTTTAAA-CGTTTTACCCA
9961 TTTTT
1 TTTTT
9966 CATTATTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTTTTTAAACGTTTTACCCA
Found at i:10864 original size:17 final size:17
Alignment explanation
Indices: 10831--10889 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
10821 GAACATTCAA
10831 AATAAATTTTAAAATTTAT
1 AATAAA-TTT-AAATTTAT
10850 AATAAATTTAAATTTCA-
1 AATAAATTTAAATTT-AT
**
10867 GCTAAATTTAAATTTAT
1 AATAAATTTAAATTTAT
10884 AATAAA
1 AATAAA
10890 CTCAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.03
17 23 0.68
18 4 0.12
19 6 0.18
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (17 bp):
AATAAATTTAAATTTAT
Found at i:15955 original size:30 final size:30
Alignment explanation
Indices: 15920--16530 Score: 395
Period size: 30 Copynumber: 20.5 Consensus size: 30
15910 ATTTTACCCA
*
15920 AAAATCACATTTTAACCCTTAAACTTCTTC
1 AAAATTACATTTTAACCCTTAAACTTCTTC
* * * * *
15950 GAAATCATATTTTGACCC-CAAAC-TCTTCC
1 AAAATTACATTTTAACCCTTAAACTTCTT-C
*
15979 AAAATTACATTTTAACCCTT-AAGTT-TTCC
1 AAAATTACATTTTAACCCTTAAACTTCTT-C
* *
16008 TAAAATTACATTTTAACCCTAAAACTTCTCC
1 -AAAATTACATTTTAACCCTTAAACTTCTTC
* *
16039 AAAATTAGATTTTAACCCCTAAACTTC-TC
1 AAAATTACATTTTAACCCTTAAACTTCTTC
*
16068 TAAAATTACATTTTAACCCCTAAACTTC-TC
1 -AAAATTACATTTTAACCCTTAAACTTCTTC
* *
16098 TAAAATCACATTTTAACCCTTAAATTTC-TC
1 -AAAATTACATTTTAACCCTTAAACTTCTTC
* *
16128 TAAAATCACATTTTAACCC-TAAACTTTTTC
1 -AAAATTACATTTTAACCCTTAAACTTCTTC
*
16158 AAAATTACATTTTAACCCTTTAA-TT-TTCCC
1 AAAATTACATTTTAACCCTTAAACTTCTT--C
* *
16188 AAAATCATATTTTAA-CCTTAAAACTTCTTC
1 AAAATTACATTTTAACCCTT-AAACTTCTTC
* * * *
16218 GAAATTAGATTTTAA-CCTTAAAATTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTCTT-C
16248 AAAATTACATTTTAATCCC-T-AACTT-TTCC
1 AAAATTACATTTTAA-CCCTTAAACTTCTT-C
* **
16277 TAAAATTACATTTTGA-CCTTAAAACTTCCCC
1 -AAAATTACATTTTAACCCTT-AAACTTCTTC
* * * ** *
16308 AAAGTTAGATTTTGACCCCCAAACTTCTCC
1 AAAATTACATTTTAACCCTTAAACTTCTTC
* * * * *
16338 AAAGTCACATTTTGA-CCTAAAAACTTCTCC
1 AAAATTACATTTTAACCCT-TAAACTTCTTC
* * * *
16368 AAAATTAGATTTTGATCCTTAAACTTCTCC
1 AAAATTACATTTTAACCCTTAAACTTCTTC
** *
16398 AAAATGGCATTTTAACCCTCAAATCTTC-TC
1 AAAATTACATTTTAACCCTTAAA-CTTCTTC
* * * *
16428 GAAATCACATTTTAA-CCTCAAACTTCTCC
1 AAAATTACATTTTAACCCTTAAACTTCTTC
** * * *
16457 AAAAACACATTATGACCC-TAAACTT-TCCC
1 AAAATTACATTTTAACCCTTAAACTTCT-TC
*
16486 AAAATTACATTTTTACTCC-TAAACTT-TTCC
1 AAAATTACATTTTAAC-CCTTAAACTTCTT-C
*
16516 AAAATTACGTTTTAA
1 AAAATTACATTTTAA
16531 TCCCAAATTC
Statistics
Matches: 475, Mismatches: 75, Indels: 62
0.78 0.12 0.10
Matches are distributed among these distances:
28 13 0.03
29 108 0.23
30 326 0.69
31 23 0.05
32 5 0.01
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTCTTC
Found at i:16225 original size:179 final size:178
Alignment explanation
Indices: 15920--16530 Score: 576
Period size: 179 Copynumber: 3.4 Consensus size: 178
15910 ATTTTACCCA
* * * * *
15920 AAAATCACATTTTAACCCTTAAACTTCTTCGAAATCATATTTTGACCCCAAACTCTTCCAAAATT
1 AAAATCACATTTTAACCCTTAAACTTCTCCAAAATCACATTTTAACCCCAAACTTTTCCAAAATT
* * *
15985 ACATTTTAACCC-TTAAGTTTTCCTAAAATTACATTTTAACCCTAAAACTTCTCCAAAATTAGAT
66 ACATTTTAACCCTTTAA-TTTTCCCAAAATTACATTTTAACCTTAAAACTTCTTCAAAATTAGAT
16049 TTTAACCCCT-AAACTTCTCTAAAATTACATTTTAACCCCTAAACTTCTCT
130 TTTAA-CCCTAAAACTTCTC-AAAATTACATTTTAACCCCTAAACTTCTCT
* * * *
16099 AAAATCACATTTTAACCCTTAAATTTCTCTAAAATCACATTTTAACCCTAAACTTTTTCAAAATT
1 AAAATCACATTTTAACCCTTAAACTTCTCCAAAATCACATTTTAACCCCAAACTTTTCCAAAATT
* * *
16164 ACATTTTAACCCTTTAATTTTCCCAAAATCATATTTTAACCTTAAAACTTCTTCGAAATTAGATT
66 ACATTTTAACCCTTTAATTTTCCCAAAATTACATTTTAACCTTAAAACTTCTTCAAAATTAGATT
* * * * *
16229 TTAACCTTAAAATTTTTCCAAAATTACATTTTAATCCCT-AACTTTTCCT
131 TTAACCCTAAAACTTCT-CAAAATTACATTTTAACCCCTAAACTTCT-CT
* * * * * * * * *
16278 AAAATTACATTTTGA-CCTTAAAACTTCCCCAAAGTTAGATTTTGACCCCCAAACTTCTCCAAAG
1 AAAATCACATTTTAACCCTT-AAACTTCTCCAAAATCACATTTT-AACCCCAAACTTTTCCAAAA
* * ** ** * * * *
16342 TCACATTTTGA-CCTAAAAACTTCTCCAAAATTAGATTTTGATCCTT-AAACTTCTCCAAAA-TG
64 TTACATTTTAACCCTTTAATTTTC-CCAAAATTACATTTT-AACCTTAAAACTTCTTCAAAATTA
* * * * *
16404 GCATTTTAACCCTCAAATCTTCTCGAAATCACATTTTAACCTC-AAACTTCTCC
127 G-ATTTTAACCCT-AAAACTTCTCAAAATTACATTTTAACCCCTAAACTTCTCT
* * * * * *
16457 AAAAACACATTATGACCC-TAAACTT-TCCCAAAATTACATTTTTACTCCTAAACTTTTCCAAAA
1 AAAATCACATTTTAACCCTTAAACTTCT-CCAAAATCACATTTTAAC-CCCAAACTTTTCCAAAA
*
16520 TTACGTTTTAA
64 TTACATTTTAA
16531 TCCCAAATTC
Statistics
Matches: 349, Mismatches: 69, Indels: 29
0.78 0.15 0.06
Matches are distributed among these distances:
177 1 0.00
178 54 0.15
179 195 0.56
180 88 0.25
181 11 0.03
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (178 bp):
AAAATCACATTTTAACCCTTAAACTTCTCCAAAATCACATTTTAACCCCAAACTTTTCCAAAATT
ACATTTTAACCCTTTAATTTTCCCAAAATTACATTTTAACCTTAAAACTTCTTCAAAATTAGATT
TTAACCCTAAAACTTCTCAAAATTACATTTTAACCCCTAAACTTCTCT
Found at i:18539 original size:9 final size:9
Alignment explanation
Indices: 18527--18572 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
18517 CCTGAGGAGA
18527 AGAAGGAAG
1 AGAAGGAAG
18536 AGAAGGAAG
1 AGAAGGAAG
18545 A-AGAGG-AG
1 AGA-AGGAAG
*
18553 AAGAATGAAG
1 -AGAAGGAAG
18563 AGAAGGAAG
1 AGAAGGAAG
18572 A
1 A
18573 TGCCCCGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 3 0.10
9 25 0.81
10 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (9 bp):
AGAAGGAAG
Found at i:18562 original size:27 final size:27
Alignment explanation
Indices: 18520--18572 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
18510 GGTAAAACCT
18520 GAGGAGAAGAAGGAAGAGAAGGAAGAA
1 GAGGAGAAGAAGGAAGAGAAGGAAGAA
*
18547 GAGGAGAAGAATGAAGAGAAGGAAGA
1 GAGGAGAAGAAGGAAGAGAAGGAAGA
18573 TGCCCCGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (27 bp):
GAGGAGAAGAAGGAAGAGAAGGAAGAA
Found at i:25769 original size:31 final size:31
Alignment explanation
Indices: 25734--25793 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
25724 AAGTATCTCA
25734 ATTTGATTTGATTCCAATCAAATTGATTTTG
1 ATTTGATTTGATTCCAATCAAATTGATTTTG
* *
25765 ATTTGGTTTGATTCTAATCAAATTGATTT
1 ATTTGATTTGATTCCAATCAAATTGATTT
25794 AAATGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.50
Consensus pattern (31 bp):
ATTTGATTTGATTCCAATCAAATTGATTTTG
Done.