Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014581.1 Kokia drynarioides strain JFW-HI SEQ_129620, 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: 8021
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1456 original size:15 final size:16
Alignment explanation
Indices: 1434--1476 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
1424 ATTTATTTTC
1434 TATTATATTTTAATAA
1 TATTATATTTTAATAA
1450 T-TTATA-TTTAA-AA
1 TATTATATTTTAATAA
1463 TATTATATTTTAAT
1 TATTATATTTTAAT
1477 CACTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 10 0.42
16 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATATTTTAATAA
Found at i:4697 original size:20 final size:21
Alignment explanation
Indices: 4672--4711 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4662 AATATTTGAA
4672 ATTTTAAAAAATATT-ATAAG
1 ATTTTAAAAAATATTGATAAG
* *
4692 ATTTTATATAATATTGATAA
1 ATTTTAAAAAATATTGATAA
4712 TTTAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTTTAAAAAATATTGATAAG
Found at i:4864 original size:23 final size:23
Alignment explanation
Indices: 4832--4877 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4822 ATATGATGAC
4832 TAAAGATATTTTTATTAAATAAAA
1 TAAAGATATTTTT-TTAAATAAAA
*
4856 TAAA-ATATTTTTTTAATTAAAA
1 TAAAGATATTTTTTTAAATAAAA
4878 AATAAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAAGATATTTTTTTAAATAAAA
Found at i:4878 original size:23 final size:25
Alignment explanation
Indices: 4832--4883 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
4822 ATATGATGAC
4832 TAAAGATATTTTTATTAAAT-AAAA
1 TAAAGATATTTTTATTAAATAAAAA
*
4856 TAAA-ATATTTTT-TTAATTAAAAAA
1 TAAAGATATTTTTATTAAAT-AAAAA
4880 TAAA
1 TAAA
4884 TGTAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 8 0.32
24 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAGATATTTTTATTAAATAAAAA
Found at i:4884 original size:23 final size:23
Alignment explanation
Indices: 4837--4884 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4827 ATGACTAAAG
*
4837 ATATTTTTATTAAATAAAATAAA
1 ATATTTTTATTAAATAAAAAAAA
*
4860 ATATTTTT-TTAATTAAAAAATAA
1 ATATTTTTATTAAATAAAAAA-AA
4883 AT
1 AT
4885 GTAAGTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATTTTTATTAAATAAAAAAAA
Found at i:5127 original size:22 final size:22
Alignment explanation
Indices: 5099--5144 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5089 TTCAGTGTGA
5099 TTGGATCACCATAAAACGTTTT
1 TTGGATCACCATAAAACGTTTT
5121 TTGGATCACCATAAAACGTTTT
1 TTGGATCACCATAAAACGTTTT
5143 TT
1 TT
5145 TTTTAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (22 bp):
TTGGATCACCATAAAACGTTTT
Found at i:6049 original size:29 final size:29
Alignment explanation
Indices: 6017--6384 Score: 292
Period size: 30 Copynumber: 12.8 Consensus size: 29
6007 AATTCAACGT
*
6017 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTTGGGGT-A
* *
6047 AAAAAGGTG-TTTTTGGAAGTTTTGGGGTT
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTA
**
6076 AAAATGGGAATTTTT-GAAGTTCGGGGGTA
1 AAAATGGG-ATTTTTGGAAGTTTTGGGGTA
* ** *
6105 AAAACGAAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGGGATTTTTGGAAGTTTTG-GGGTA
* * *
6135 AAAATGGGTTTTTTTTGGAAGTTTTAGGGTC
1 AAAATGGG--ATTTTTGGAAGTTTTGGGGTA
*
6166 AAAA----A----TGGAATTTTTGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTTGGGGT-A
*
6188 AAAATGGGATTTTTGGAAG-TTAGGGGTA
1 AAAATGGGATTTTTGGAAGTTTTGGGGTA
* * * *
6216 AAAACGAGATTTTTGGAAGTTTCGAGTGTA
1 AAAATGGGATTTTTGGAAGTTTTG-GGGTA
** *
6246 AAAATGAAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGGATTTTTGGAAGTTTT-GGGGTA
* * *
6276 AAAATGAGAATTTTGGAAGTTTAGGGGTA
1 AAAATGGGATTTTTGGAAGTTTTGGGGTA
* *
6305 AAAATGGAATTTTTAGAAGTTTTGGGGTTA
1 AAAATGGGATTTTTGGAAGTTTTGGGG-TA
* *
6335 AAAATGAGATTTTTGGAAG-TTCGGGGTA
1 AAAATGGGATTTTTGGAAGTTTTGGGGTA
* *
6363 AAAAAGGAATTTTTGGAAGTTT
1 AAAATGGGATTTTTGGAAGTTT
6385 AGGGACTTTC
Statistics
Matches: 266, Mismatches: 51, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
21 13 0.05
22 4 0.02
26 1 0.00
28 43 0.16
29 74 0.28
30 108 0.41
31 9 0.03
32 14 0.05
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTTTGGGGTA
Found at i:6199 original size:21 final size:21
Alignment explanation
Indices: 6150--6203 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6140 GGGTTTTTTT
* *
6150 TGGAAGTTTTAGGGTCAAAAA
1 TGGAATTTTTGGGGTCAAAAA
6171 TGGAATTTTTGGGGTCAAAAA
1 TGGAATTTTTGGGGTCAAAAA
*
6192 TGGGATTTTTGG
1 TGGAATTTTTGG
6204 AAGTTAGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (21 bp):
TGGAATTTTTGGGGTCAAAAA
Found at i:6200 original size:111 final size:109
Alignment explanation
Indices: 6060--6388 Score: 321
Period size: 111 Copynumber: 2.9 Consensus size: 109
6050 AAGGTGTTTT
* * *
6060 TGGAAGTTTTGGGGTTAAAATGGGAATTTTT-GAAGTTCGGGGGTAAAAACGAAATTTTTGGAAG
1 TGGAATTTTTGGGGTAAAAATGGGAATTTTTGGAAGTT-AGGGGTAAAAACGAAATTTTTGGAAG
* ***
6124 TTTTGAG-GTTAAAAATGGGTTTTTTTTGGAAGTTTTAGGGTCAAAAA
65 TTTCGAGTG-TAAAAAT--GAAATTTTTGGAAGTTTTAGGGTCAAAAA
*
6171 TGGAATTTTTGGGGTCAAAAATGGG-ATTTTTGGAAGTTAGGGGTAAAAACGAGATTTTTGGAAG
1 TGGAATTTTTGGGGT-AAAAATGGGAATTTTTGGAAGTTAGGGGTAAAAACGAAATTTTTGGAAG
*
6235 TTTCGAGTGTAAAAATGAAATTTTTGGAAGTTTTAGGGTTAAAAA
65 TTTCGAGTGTAAAAATGAAATTTTTGGAAGTTTTAGGGTCAAAAA
* * * *
6280 TGAGAATTTTGGAAGTTTAGGGGTAAAAAT-GGAATTTTTAGAAGTTTTGGGGTTAAAAATGAGA
1 TG-GAA--TT-----TTT-GGGGTAAAAATGGGAATTTTTGGAAG-TTAGGGG-TAAAAACGAAA
* * *
6344 TTTTTGGAAG-TTCG-GGGTAAAAAAGGAATTTTTGGAAG-TTTAGGG
55 TTTTTGGAAGTTTCGAGTGTAAAAATGAAATTTTTGGAAGTTTTAGGG
6389 ACTTTCGGAG
Statistics
Matches: 188, Mismatches: 15, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
109 27 0.14
110 3 0.02
111 57 0.30
112 17 0.09
116 9 0.05
117 40 0.21
118 15 0.08
119 20 0.11
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.36
Consensus pattern (109 bp):
TGGAATTTTTGGGGTAAAAATGGGAATTTTTGGAAGTTAGGGGTAAAAACGAAATTTTTGGAAGT
TTCGAGTGTAAAAATGAAATTTTTGGAAGTTTTAGGGTCAAAAA
Found at i:6327 original size:59 final size:58
Alignment explanation
Indices: 6171--6388 Score: 278
Period size: 58 Copynumber: 3.7 Consensus size: 58
6161 GGGTCAAAAA
* * * * *
6171 TGGAATTTTTGGGGTCAAAAATGGGATTTTTGGAAG-TTAGGGGTAAAAACGAGATTTT
1 TGGAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAGTTTAGGGTTAAAAATGAGATTTT
* * *
6229 TGGAAGTTTCGAGTGTAAAAATGAAATTTTTGGAAGTTTTAGGGTTAAAAATGAGAATTT
1 TGGAAGTTTCG-GGGTAAAAATGGAATTTTTGGAAG-TTTAGGGTTAAAAATGAGATTTT
* * *
6289 TGGAAGTTTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGAGATTTT
1 TGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAG-TTTAGGGTTAAAAATGAGATTTT
*
6348 TGGAAG-TTCGGGGTAAAAAAGGAATTTTTGGAAGTTTAGGG
1 TGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTAGGG
6389 ACTTTCGGAG
Statistics
Matches: 139, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
57 6 0.04
58 52 0.37
59 52 0.37
60 29 0.21
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (58 bp):
TGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGTTAAAAATGAGATTTT
Done.