Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014312.1 Kokia drynarioides strain JFW-HI SEQ_129349, 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: 27137
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:48 original size:6 final size:6
Alignment explanation
Indices: 3--80 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
1 AT
* * *
3 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
50 TTTAAA -ATAAA TTTAAA TTT-AA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
81 TTAAAAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.25
6 37 0.65
7 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:65 original size:17 final size:17
Alignment explanation
Indices: 3--111 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 17
1 AT
* *
3 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
20 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
38 TTTAAACTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
56 -ATAAATTTAAATTTAA
1 TTTAAATTTAAAATAAA
*
72 TTTAAATTTTTAAA-AAA
1 TTTAAA-TTTAAAATAAA
89 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
106 TTTAAA
1 TTTAAA
112 GGGGAGTTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
15 1 0.01
16 11 0.15
17 36 0.49
18 25 0.34
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:80 original size:11 final size:11
Alignment explanation
Indices: 21--79 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
11 TATAATAATT
21 TTAAATTTGAAA
1 TTAAATTT-AAA
*
33 ATAAATTTAAA
1 TTAAATTTAAA
44 CTTAAATTTAAA
1 -TTAAATTTAAA
*
56 ATAAATTTAAA
1 TTAAATTTAAA
*
67 TTTAATTTAAA
1 TTAAATTTAAA
78 TT
1 TT
80 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 24 0.59
12 17 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:949 original size:120 final size:120
Alignment explanation
Indices: 736--991 Score: 442
Period size: 120 Copynumber: 2.1 Consensus size: 120
726 AGGGAGATGG
* * * *
736 TCAGGAAGCTGACCGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTTGAGATTT
1 TCAGGAAGATGACCGTTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAGTAGAGATTC
801 GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTATTCTTCTCAGTATCTCA
66 GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTATTCTTCTCAGTATCTCA
*
856 TCAGGAAGATAACCGTTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAGCTAG-GATT
1 TCAGGAAGATGACCGTTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAG-TAGAGATT
*
920 CGAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCA
65 CGAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTATTCTTCTCAGTATCTCA
976 TCAGGAAGATGACCGT
1 TCAGGAAGATGACCGT
992 GTCGTTTTGT
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
120 126 0.98
121 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (120 bp):
TCAGGAAGATGACCGTTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAGTAGAGATTC
GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTATTCTTCTCAGTATCTCA
Found at i:1527 original size:26 final size:28
Alignment explanation
Indices: 1478--1538 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
1468 CCAAGAATTC
*
1478 TATTAAAAAGAGGATCGAAGGAAA-CAA
1 TATTAAAAAGAGGATCGAAAGAAAGCAA
*
1505 TATTAAAAAGAGGGTC-AAAGAAAGCAA
1 TATTAAAAAGAGGATCGAAAGAAAGCAA
1532 TAATTAA
1 T-ATTAA
1539 TTGAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 6 0.20
27 19 0.63
28 5 0.17
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (28 bp):
TATTAAAAAGAGGATCGAAAGAAAGCAA
Found at i:7172 original size:26 final size:28
Alignment explanation
Indices: 7123--7183 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
7113 CCAAGAATTC
*
7123 TATTAAAAAGAGGATCGAAGGAAA-CAA
1 TATTAAAAAGAGGATCGAAAGAAAGCAA
*
7150 TATTAAAAAGAGGGTC-AAAGAAAGCAA
1 TATTAAAAAGAGGATCGAAAGAAAGCAA
7177 TAATTAA
1 T-ATTAA
7184 TTGAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 6 0.20
27 19 0.63
28 5 0.17
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (28 bp):
TATTAAAAAGAGGATCGAAAGAAAGCAA
Found at i:24101 original size:29 final size:28
Alignment explanation
Indices: 24065--24385 Score: 237
Period size: 30 Copynumber: 11.0 Consensus size: 28
24055 CGGATGCACG
* *
24065 GGGGCAAAATGGTAGTTTTGGAAGGTTC
1 GGGGTAAAATGGTATTTTTGGAAGGTTC
*
24093 GGAGTCAAAAATGAG-ATTTTTGGAA-GTTC
1 GGGGT--AAAATG-GTATTTTTGGAAGGTTC
* *
24122 GAGGGTAAAATGGTAATTTTCGAAAGGTTC
1 G-GGGTAAAATGGT-ATTTTTGGAAGGTTC
24152 GGGGTCAAAAATGAG-ATTTTTGGAA-GTTC
1 GGGGT--AAAATG-GTATTTTTGGAAGGTTC
*
24181 GGGGGTAAAATGGTAATTTTTAGAAGGTTC
1 -GGGGTAAAATGGT-ATTTTTGGAAGGTTC
* * *
24211 GAGGTCAAAGATGGGATTTTTGG-ATGTTC
1 GGGGT-AAA-ATGGTATTTTTGGAAGGTTC
*
24240 GGGGGT-AAATGGTAATTTTTAGAAGGTTC
1 -GGGGTAAAATGGT-ATTTTTGGAAGGTTC
*
24269 GGGGTTAAAAATGGGATTTTTGGAA-GTTC
1 GGGG-T-AAAATGGTATTTTTGGAAGGTTC
*
24298 GGGGGTAAAATGGTAATTTTTAGAAGGTTC
1 -GGGGTAAAATGGT-ATTTTTGGAAGGTTC
*
24328 GAGGTTAAAAATGAG-ATTTTTGGAA-GTTC
1 G-GGGT-AAAATG-GTATTTTTGGAAGGTTC
* *
24357 GGGGGTAAAATGGTAAATTTTCGAAGGTT
1 -GGGGTAAAATGGT-ATTTTTGGAAGGTT
24386 TGAAAACTAT
Statistics
Matches: 235, Mismatches: 26, Indels: 62
0.73 0.08 0.19
Matches are distributed among these distances:
27 7 0.03
28 41 0.17
29 75 0.32
30 87 0.37
31 23 0.10
32 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (28 bp):
GGGGTAAAATGGTATTTTTGGAAGGTTC
Found at i:24152 original size:59 final size:59
Alignment explanation
Indices: 24063--24385 Score: 433
Period size: 59 Copynumber: 5.5 Consensus size: 59
24053 TTCGGATGCA
* *
24063 CGGGGGCAAAATGGTAGTTTTG-GAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
* *
24121 CGAGGGTAAAATGGTAATTTTCGA-AAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTT-GAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
* * * *
24180 CGGGGGTAAAATGGTAATTTTTAGAAGGTTC-GAGGTCAAAGATGGGATTTTTGGATGTT
1 CGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGA-GTCAAAAATGAGATTTTTGGAAGTT
* * * *
24239 CGGGGGT-AAATGGTAATTTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
* *
24297 CGGGGGTAAAATGGTAATTTTTAGAAGGTTC-GAGGTTAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGA-GTCAAAAATGAGATTTTTGGAAGTT
*
24356 CGGGGGTAAAATGGTAAATTTT-CGAAGGTT
1 CGGGGGTAAAATGGT-AATTTTGAGAAGGTT
24386 TGAAAACTAT
Statistics
Matches: 240, Mismatches: 17, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
58 73 0.30
59 161 0.67
60 6 0.03
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
Found at i:24266 original size:117 final size:117
Alignment explanation
Indices: 24063--24385 Score: 490
Period size: 117 Copynumber: 2.8 Consensus size: 117
24053 TTCGGATGCA
* * * *
24063 CGGGGGCAAAATGGT-AGTTTTGGAAGGTTCG-GAGTCAAAAATGAGATTTTTGGAAGTTCGAGG
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAG-GTCAAAAATGAGATTTTTGGAAGTTCGGGG
24126 GTAAAATGGTAATTTTCGAAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTT
65 GTAAAATGGTAATTTTCG-AAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTT
* * *
24180 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAGATGGGATTTTTGGATGTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGG
* * *
24245 T-AAATGGTAATTTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
66 TAAAATGGTAA-TTTTCGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTT
*
24297 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTTAAAAATGAGATTTTTGGAAGTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGG
24362 TAAAATGGTAAATTTTCGAAGGTT
66 TAAAATGGT-AATTTTCGAAGGTT
24386 TGAAAACTAT
Statistics
Matches: 186, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
117 118 0.63
118 65 0.35
119 3 0.02
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGG
TAAAATGGTAATTTTCGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTT
Found at i:25131 original size:21 final size:23
Alignment explanation
Indices: 25096--25139 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
25086 TAAAAAAGAA
25096 CAGATCTAGGCCTAGATC-AAAC
1 CAGATCTAGGCCTAGATCTAAAC
25118 CAGATCTA-GCCTAGATCTAAAC
1 CAGATCTAGGCCTAGATCTAAAC
25140 GGTTTTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (23 bp):
CAGATCTAGGCCTAGATCTAAAC
Found at i:25490 original size:16 final size:16
Alignment explanation
Indices: 25471--25503 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25461 TCATTAATGT
25471 CACCATTTATTACTGC
1 CACCATTTATTACTGC
25487 CACCATTTATTACTGC
1 CACCATTTATTACTGC
25503 C
1 C
25504 CTCTATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CACCATTTATTACTGC
Found at i:26194 original size:17 final size:17
Alignment explanation
Indices: 26174--26221 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
26164 TTTGAACTTT
*
26174 ATTTTAAATTTATAATA
1 ATTTTAAATTTAAAATA
26191 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
*
26209 AATTTAAATTTAA
1 ATTTTAAATTTAA
26222 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:26229 original size:46 final size:45
Alignment explanation
Indices: 26171--26261 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 45
26161 TTATTTGAAC
* * * *
26171 TTTATTTTAAATTTATAATAATTTTAAAT-TTGAAAATAAATTTAAA
1 TTTAATTTAAATTTATAACAAATTT-AATCTT-AAAATAAAATTAAA
*
26217 TTTAATTTAAATTTTTAACAAATTTAATCTTAAAATAAAATTAAA
1 TTTAATTTAAATTTATAACAAATTTAATCTTAAAATAAAATTAAA
26262 GGGGAGTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 16 0.41
46 23 0.59
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (45 bp):
TTTAATTTAAATTTATAACAAATTTAATCTTAAAATAAAATTAAA
Done.