Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006483.1 Kokia drynarioides strain JFW-HI SEQ_121066, 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: 35833
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Found at i:148 original size:29 final size:30
Alignment explanation
Indices: 18--146 Score: 156
Period size: 29 Copynumber: 4.4 Consensus size: 30
8 AAATTTCATC
* **
18 TTAACCCTTAAACTTTCCTAAAATCACATT
1 TTAACCCCTAAACTTTTTTAAAATCACATT
*
48 TTAACCCC-AAACTTTCTTAAAATCACATT
1 TTAACCCCTAAACTTTTTTAAAATCACATT
** *
77 TTAA-CCCTAAACTTTTACAAAATTACATT
1 TTAACCCCTAAACTTTTTTAAAATCACATT
* *
106 TTAACCCCTAAATTTTTTTAAAATTACATT
1 TTAACCCCTAAACTTTTTTAAAATCACATT
136 TT-ACCCCTAAA
1 TTAACCCCTAAA
147 TTCTCTAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
28 3 0.03
29 54 0.61
30 31 0.35
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (30 bp):
TTAACCCCTAAACTTTTTTAAAATCACATT
Found at i:164 original size:28 final size:30
Alignment explanation
Indices: 4--165 Score: 153
Period size: 29 Copynumber: 5.5 Consensus size: 30
1 TTT
* * *
4 TCTAAAATTTCATCTTAACCCTTAAACTTTC
1 TCTAAAATTACATTTTAACCCCTAAA-TTTC
*
35 -CTAAAATCACATTTTAACCCC-AAACTTTC
1 TCTAAAATTACATTTTAACCCCTAAA-TTTC
*
64 T-TAAAATCACATTTTAA-CCCTAAACTTT-
1 TCTAAAATTACATTTTAACCCCTAAA-TTTC
*
92 TAC-AAAATTACATTTTAACCCCTAAATTTT
1 T-CTAAAATTACATTTTAACCCCTAAATTTC
*
122 TTTAAAATTACATTTT-ACCCCTAAA-TTC
1 TCTAAAATTACATTTTAACCCCTAAATTTC
150 TCTAAAACTT-CATTTT
1 TCTAAAA-TTACATTTT
166 TAACTCTTTT
Statistics
Matches: 115, Mismatches: 8, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
28 18 0.16
29 59 0.51
30 38 0.33
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.40
Consensus pattern (30 bp):
TCTAAAATTACATTTTAACCCCTAAATTTC
Found at i:169 original size:59 final size:58
Alignment explanation
Indices: 18--146 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 58
8 AAATTTCATC
* *
18 TTAACCCTTAAAC-TTTCCTAAAATCACATTTTAACCCCAAACTTTCTTAAAATCACATT
1 TTAACCC-TAAACTTTTAC-AAAATTACATTTTAACCCCAAACTTTCTTAAAATCACATT
* * *
77 TTAACCCTAAACTTTTACAAAATTACATTTTAACCCCTAAATTTTTTTAAAATTACATT
1 TTAACCCTAAACTTTTACAAAATTACATTTTAACCCC-AAACTTTCTTAAAATCACATT
*
136 TTACCCCTAAA
1 TTAACCCTAAA
147 TTCTCTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 23 0.37
59 39 0.63
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (58 bp):
TTAACCCTAAACTTTTACAAAATTACATTTTAACCCCAAACTTTCTTAAAATCACATT
Found at i:3823 original size:50 final size:50
Alignment explanation
Indices: 3728--3823 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
3718 ACACTTCTAT
* * * * *
3728 CGATACAACGAGTTCTAGAGAGCTAGGAAAGATTTTCTTGTAACTTTTAC
1 CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTTTTAC
3778 CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTT
1 CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTT
3824 CCACTGATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (50 bp):
CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTTTTAC
Found at i:3833 original size:50 final size:50
Alignment explanation
Indices: 3728--3835 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
3718 ACACTTCTAT
* * * * * **
3728 CGATACAACGAGTTCTAGAGAGCTAGGAAAGATTTTCTTGTAACTTTTAC
1 CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTTCCAC
3778 CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTTCCAC
1 CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTTCCAC
*
3828 TGATACAA
1 CGATACAA
3836 GTGATACAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (50 bp):
CGATACAACGAGTTCAAAAGAGCTAGGAAAGATTTCCCTGCAACTTCCAC
Found at i:7412 original size:49 final size:50
Alignment explanation
Indices: 7318--7412 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 50
7308 TGCATCCATT
* * * * *
7318 TAAAGGTTGAAAAACCTTATTCTAATAAATATTAAATAGATGAAGTATAG
1 TAAAGGTTAAAAAAACTTATTCTAATAAATATCAAATAAAAGAAGTATAG
* *
7368 TAAA-GTTAAAAAAACTTATTCTAATCAATGTCAAATAAAAGAAGT
1 TAAAGGTTAAAAAAACTTATTCTAATAAATATCAAATAAAAGAAGT
7413 GTAATTATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 34 0.89
50 4 0.11
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (50 bp):
TAAAGGTTAAAAAAACTTATTCTAATAAATATCAAATAAAAGAAGTATAG
Found at i:9008 original size:15 final size:15
Alignment explanation
Indices: 8990--9036 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
8980 TTTTTTCATA
8990 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
9005 TTATATTTGAAATA-
1 TTATATTTTAATTAT
* *
9019 TTATATTGTAATCAT
1 TTATATTTTAATTAT
9034 TTA
1 TTA
9037 CGTTAGTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:9568 original size:18 final size:19
Alignment explanation
Indices: 9544--9593 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
9534 TTTCAAAAAT
*
9544 ATAAAAAATTATT-TTAAT
1 ATAAAAAATTATTATTAAG
* *
9562 TTAAAAAAATATTATTAAG
1 ATAAAAAATTATTATTAAG
9581 ATAATAAAATTAT
1 ATAA-AAAATTAT
9594 ATTTTTACTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 11 0.44
19 7 0.28
20 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAAAAATTATTATTAAG
Found at i:9570 original size:19 final size:20
Alignment explanation
Indices: 9546--9593 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
9536 TCAAAAATAT
**
9546 AAAAAATTATT-TTAATTTA
1 AAAAAATTATTATTAAGATA
9565 AAAAAA-TATTATTAAGATA
1 AAAAAATTATTATTAAGATA
*
9584 ATAAAATTAT
1 AAAAAATTAT
9594 ATTTTTACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 17 0.71
20 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAAAATTATTATTAAGATA
Found at i:9589 original size:20 final size:20
Alignment explanation
Indices: 9566--9616 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
9556 TTTAATTTAA
9566 AAAAATATTATTAAGATAAT
1 AAAAATATTATTAAGATAAT
* **
9586 AAAATTATATTTTTACTATAAT
1 AAAA--ATATTATTAAGATAAT
9608 AAAAATATT
1 AAAAATATT
9617 CAATTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
22 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAATATTATTAAGATAAT
Found at i:12518 original size:16 final size:16
Alignment explanation
Indices: 12499--12546 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
12489 AGAACAACAT
12499 TTGTTTAGAATAGTTC
1 TTGTTTAGAATAGTTC
* *
12515 TTGTTTAGAATAATTT
1 TTGTTTAGAATAGTTC
*
12531 TTGTTTGATAATAGTT
1 TTGTTT-AGAATAGTT
12547 ATGTTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (16 bp):
TTGTTTAGAATAGTTC
Found at i:16488 original size:82 final size:83
Alignment explanation
Indices: 16345--16512 Score: 320
Period size: 82 Copynumber: 2.0 Consensus size: 83
16335 ATGATGTTTT
*
16345 AACTATCTCACCTATATTTCAAGAGACCTTAAAAAAGTTTCGATTCTTTCATATTCGCCAGATAA
1 AACTATCTCACCTATATTTCAAGAGACCTTAAAAAAGTTTCGATTCTTTCATATTCACCAGATAA
16410 GTAAACCAAACAAACAAG
66 GTAAACCAAACAAACAAG
16428 AACT-TCTCACCTATATTTCAAGAGACCTTAAAAAAGTTTCGATTCTTTCATATTCACCAGATAA
1 AACTATCTCACCTATATTTCAAGAGACCTTAAAAAAGTTTCGATTCTTTCATATTCACCAGATAA
16492 GTAAACCAAACAAACAAG
66 GTAAACCAAACAAACAAG
16510 AAC
1 AAC
16513 AAATTATCTC
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 80 0.95
83 4 0.05
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (83 bp):
AACTATCTCACCTATATTTCAAGAGACCTTAAAAAAGTTTCGATTCTTTCATATTCACCAGATAA
GTAAACCAAACAAACAAG
Found at i:18085 original size:27 final size:22
Alignment explanation
Indices: 18026--18074 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
18016 AGATAAAATT
18026 TTTATTTA-TTTTAATTTAATC
1 TTTATTTATTTTTAATTTAATC
18047 TTTATTTATTTTTAATTTAATC
1 TTTATTTATTTTTAATTTAATC
18069 TTTATT
1 TTTATT
18075 GAATATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTTATTTTTAATTTAATC
Found at i:35817 original size:17 final size:17
Alignment explanation
Indices: 35795--35827 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35785 AACTTTTCTT
*
35795 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAAATTAAA
35812 TTAAGTTTAAAATTAA
1 TTAAGTTTAAAATTAA
35828 TTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTAAGTTTAAAATTAAA
Done.