Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013463.1 Kokia drynarioides strain JFW-HI SEQ_128489, 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: 6038
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Found at i:2575 original size:28 final size:28
Alignment explanation
Indices: 2543--2602 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
2533 CAATTTTAAA
* *
2543 TTAATTATTATTTTCTTTGACCCTCTTT
1 TTAATTATTACTTCCTTTGACCCTCTTT
* * *
2571 TTAA-TATTGCTTCCTTTGATCCTTTTT
1 TTAATTATTACTTCCTTTGACCCTCTTT
2598 TTAAT
1 TTAAT
2603 AGAATTCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.18, C:0.17, G:0.05, T:0.60
Consensus pattern (28 bp):
TTAATTATTACTTCCTTTGACCCTCTTT
Found at i:3491 original size:218 final size:219
Alignment explanation
Indices: 3094--3858 Score: 1117
Period size: 218 Copynumber: 3.5 Consensus size: 219
3084 ATTATCCACA
* ** *
3094 AAACAACGCAGTCATCTTCCCGATGAGATACT-GAGAAGAAGACTGAATCAAACCCATGCTCGAT
1 AAACGACGCAGTCATCTTCCCGATGAGATACTAGAGAAGAAGACCAAATCAAACCCACGCTCGAT
* * * **
3158 ATGAGCAAAACTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTATCGAAGTAATAAGAC
66 GTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGAC
* * * *
3223 GGTTGGTTTCCTGGCCATCTTCCTAATGAGGTACGGAGAAGTGGACCAAATTCCTCTTCCTGATG
131 GGTTGGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGATG
3288 AGATACAGAGAAGTGAATTGAAAC
196 AGATACAGAGAAGTGAATTGAAAC
* * * * * * *
3312 AAATGATGCGGTCATCTTCCTGATGAGACACTAG-GAAGAGGACCAAACCAAACCCACGCTCGAT
1 AAACGACGCAGTCATCTTCCCGATGAGATACTAGAGAAGAAGACCAAATCAAACCCACGCTCGAT
*
3376 GTGAGCAAATCTTTGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGAC
66 GTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGAC
* * *
3441 GGTTGGCTTCCTGACCATCTTCTTGATGAGGTACGGAAAAGTGAACCAAATTCGTCTTCCTGATG
131 GGTTGGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGATG
3506 AGATACAGAGAAGTGAATTGAAAC
196 AGATACAGAGAAGTGAATTGAAAC
* * * * *
3530 AAACGACGCAGTCATCTTCCCGATGAAATAC-CGAGAAGAAGACCGAATCAAACCCATGCTCAAT
1 AAACGACGCAGTCATCTTCCCGATGAGATACTAGAGAAGAAGACCAAATCAAACCCACGCTCGAT
* * *
3594 GTGAGCAAATCTTCAAACTATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGAC
66 GTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGAC
* *
3659 GGTTGACTTCTTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGATG
131 GGTTGGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGATG
3724 AGATACAGAGAAGTGAATTGAAAC
196 AGATACAGAGAAGTGAATTGAAAC
* * ** *
3748 AAACGACACAGTCATCTTCCCGATGAGATACTA-AAAAGAAGACCAAATCAAACTTAC-ATCCGA
1 AAACGACGCAGTCATCTTCCCGATGAGATACTAGAGAAGAAGACCAAATCAAACCCACGCT-CGA
* *
3811 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGC
65 TGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGC
3859 AGGTCGAAGC
Statistics
Matches: 483, Mismatches: 60, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
217 2 0.00
218 480 0.99
219 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (219 bp):
AAACGACGCAGTCATCTTCCCGATGAGATACTAGAGAAGAAGACCAAATCAAACCCACGCTCGAT
GTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGAC
GGTTGGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGATG
AGATACAGAGAAGTGAATTGAAAC
Found at i:4420 original size:17 final size:17
Alignment explanation
Indices: 4394--4427 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4384 AAATTATGAG
4394 TTTGAATTTAATTTAAA
1 TTTGAATTTAATTTAAA
* *
4411 TTTGAGTTTATTTTAAA
1 TTTGAATTTAATTTAAA
4428 CTAAAATTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTGAATTTAATTTAAA
Found at i:5155 original size:19 final size:21
Alignment explanation
Indices: 5131--5171 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5121 ATCAGGTGCA
5131 TTTATT-TTAA-AGTATTAAT
1 TTTATTATTAACAGTATTAAT
5150 TTTATTATTAATCAGTATTAAT
1 TTTATTATTAA-CAGTATTAAT
5172 AATAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
22 9 0.47
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTATTATTAACAGTATTAAT
Found at i:5185 original size:15 final size:15
Alignment explanation
Indices: 5165--5209 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
5155 TATTAATCAG
5165 TATTAATAATAATAA
1 TATTAATAATAATAA
*
5180 TATTAATAATATTAA
1 TATTAATAATAATAA
5195 TGACATTAATAATAA
1 T---ATTAATAATAA
5210 ATGGGGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 15 0.60
18 10 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TATTAATAATAATAA
Found at i:5186 original size:9 final size:9
Alignment explanation
Indices: 5168--5208 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
5158 TAATCAGTAT
*
5168 TAATAATAA
1 TAATATTAA
5177 TAATATTAA
1 TAATATTAA
5186 TAATATTAA
1 TAATATTAA
* *
5195 TGACATTAA
1 TAATATTAA
5204 TAATA
1 TAATA
5209 AATGGGGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (9 bp):
TAATATTAA
Found at i:5425 original size:46 final size:46
Alignment explanation
Indices: 5369--5465 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
5359 AATTGTACCG
* *
5369 AATAAAAGTTCATGTATCAAATTATATATTGAACAAAAATTGATAT
1 AATAAAAGTTCATGTATCAAATTATACATTGAACAAAAATTAATAT
* *
5415 AATAATAGTTCATGTATCAAATTATACATTGAACCAAAATTAATAT
1 AATAAAAGTTCATGTATCAAATTATACATTGAACAAAAATTAATAT
5461 -ATAAA
1 AATAAA
5466 TTTGATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.09
46 42 0.91
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (46 bp):
AATAAAAGTTCATGTATCAAATTATACATTGAACAAAAATTAATAT
Done.